diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4_diagrams.md b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4_diagrams.md
new file mode 100644
index 000000000..5dd96cf20
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Assembly-Hifi-HiC-phasing-VGP4/Assembly-Hifi-HiC-phasing-VGP4_diagrams.md
@@ -0,0 +1,168 @@
+# Workflow diagrams
+
+## Assembly-Hifi-HiC-phasing-VGP4
+
+```mermaid
+graph LR
+0["Pacbio Reads Collection"]@{ shape: docs }
+1["HiC forward reads"]@{ shape: doc }
+2["HiC reverse reads"]@{ shape: doc }
+3["Genomescope Summary"]@{ shape: doc }
+4["Meryl Database"]@{ shape: doc }
+5["Database for Busco Lineage"]@{ shape: lean-l }
+6["Lineage"]@{ shape: lean-l }
+7["Name for Haplotype 1"]@{ shape: lean-l }
+8["Name for Haplotype 2"]@{ shape: lean-l }
+9["Bits for bloom filter"]@{ shape: lean-l }
+10["SAK input file"]@{ shape: doc }
+11["Homozygous Read Coverage"]@{ shape: lean-l }
+12["Genomescope Model Parameters"]@{ shape: doc }
+13["Cutadapt"]@{ shape: process }
+0 --> 13
+14["Search in textfiles"]@{ shape: process }
+3 --> 14
+15["Compute"]@{ shape: process }
+12 --> 15
+16["MultiQC"]@{ shape: process }
+13 --> 16
+17["Replace Text"]@{ shape: process }
+14 --> 17
+18["Cut"]@{ shape: process }
+15 --> 18
+19["Convert"]@{ shape: process }
+17 --> 19
+20["Estimated homozygous read coverage"]@{ shape: process }
+18 --> 20
+21["Cut"]@{ shape: process }
+19 --> 21
+22["Homozygous read coverage for Hifiasm"]@{ shape: process }
+11 --> 22
+20 --> 22
+23["Estimated genome size"]@{ shape: process }
+21 --> 23
+24["Hifiasm"]@{ shape: process }
+22 --> 24
+9 --> 24
+1 --> 24
+2 --> 24
+13 --> 24
+25["Raw Unitig Image"]@{ shape: process }
+24 --> 25
+26["gfastats"]@{ shape: process }
+24 --> 26
+23 --> 26
+27["gfastats"]@{ shape: process }
+24 --> 27
+23 --> 27
+28["gfastats"]@{ shape: process }
+24 --> 28
+29["gfastats"]@{ shape: process }
+24 --> 29
+30["gfastats"]@{ shape: process }
+24 --> 30
+31["gfastats"]@{ shape: process }
+24 --> 31
+32["gfastats"]@{ shape: process }
+24 --> 32
+10 --> 32
+33["gfastats"]@{ shape: process }
+24 --> 33
+10 --> 33
+34["Text reformatting"]@{ shape: process }
+26 --> 34
+35["Text reformatting"]@{ shape: process }
+27 --> 35
+36["Data Prep Hap2"]@{ shape: subprocess }
+28 --> 36
+37["Data Prep Hap1"]@{ shape: subprocess }
+30 --> 37
+38["Text transformation"]@{ shape: process }
+32 --> 38
+39["Text transformation"]@{ shape: process }
+33 --> 39
+40["Join two Datasets"]@{ shape: process }
+35 --> 40
+34 --> 40
+41["Plot Data"]@{ shape: subprocess }
+36 --> 41
+8 --> 41
+7 --> 41
+37 --> 41
+42["Busco"]@{ shape: process }
+38 --> 42
+5 --> 42
+6 --> 42
+43["Merqury"]@{ shape: process }
+39 --> 43
+38 --> 43
+4 --> 43
+44["Busco"]@{ shape: process }
+39 --> 44
+5 --> 44
+6 --> 44
+45["Advanced Cut"]@{ shape: process }
+40 --> 45
+46["output_merqury.spectra-cn.fl"]@{ shape: process }
+43 --> 46
+47["output_merqury.spectra-asm.fl"]@{ shape: process }
+43 --> 47
+48["merqury_qv"]@{ shape: process }
+43 --> 48
+49["output_merqury.assembly_01.spectra-cn.fl"]@{ shape: process }
+43 --> 49
+50["merqury_stats"]@{ shape: process }
+43 --> 50
+51["output_merqury.assembly_02.spectra-cn.fl"]@{ shape: process }
+43 --> 51
+52["Replace"]@{ shape: process }
+45 --> 52
+```
+
+## gfastats_plot
+
+```mermaid
+graph LR
+0["Primary data"]@{ shape: doc }
+1["Alternate data"]@{ shape: doc }
+2["Name of primary assembly"]@{ shape: lean-l }
+3["Name of alternate assembly"]@{ shape: lean-l }
+4["Add column"]@{ shape: process }
+2 --> 4
+0 --> 4
+5["Add column"]@{ shape: process }
+3 --> 5
+1 --> 5
+6["Concatenate datasets"]@{ shape: process }
+4 --> 6
+5 --> 6
+7["Cut"]@{ shape: process }
+6 --> 7
+8["Cut"]@{ shape: process }
+6 --> 8
+9["Nx Plot"]@{ shape: process }
+7 --> 9
+10["Size Plot"]@{ shape: process }
+8 --> 10
+```
+
+## gfastats_data_prep
+
+```mermaid
+graph LR
+0["gfa_stats"]@{ shape: doc }
+1["Sort"]@{ shape: process }
+0 --> 1
+2["Text reformatting"]@{ shape: process }
+1 --> 2
+3["Datamash"]@{ shape: process }
+2 --> 3
+4["Add column"]@{ shape: process }
+2 --> 4
+5["Parse parameter value"]@{ shape: process }
+3 --> 5
+6["Compose text parameter value"]@{ shape: process }
+5 --> 6
+7["Compute"]@{ shape: process }
+4 --> 7
+6 --> 7
+```
diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5_diagrams.md b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5_diagrams.md
new file mode 100644
index 000000000..34e326dfe
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Assembly-Hifi-Trio-phasing-VGP5/Assembly-Hifi-Trio-phasing-VGP5_diagrams.md
@@ -0,0 +1,172 @@
+# Workflow diagrams
+
+## Assembly-Hifi-Trio-phasing-VGP5
+
+```mermaid
+graph LR
+0["Pacbio Reads Collection : child"]@{ shape: docs }
+1["Paternal Illumina reads (hap1)"]@{ shape: docs }
+2["Maternal Illumina reads (hap2)"]@{ shape: docs }
+3["Meryl Database : Child"]@{ shape: doc }
+4["Hapmer Database : Paternal"]@{ shape: doc }
+5["Hapmer Database : Maternal"]@{ shape: doc }
+6["Bits for bloom filter"]@{ shape: lean-l }
+7["Database for Busco Lineage"]@{ shape: lean-l }
+8["Lineage"]@{ shape: lean-l }
+9["Homozygous Read Coverage"]@{ shape: lean-l }
+10["Genomescope Model Parameters"]@{ shape: doc }
+11["Genomescope Summary"]@{ shape: doc }
+12["Utilize homology information to correct trio-phasing errors"]@{ shape: lean-l }
+13["SAK input file (Optional)"]@{ shape: doc }
+14["Name for Haplotype 1"]@{ shape: lean-l }
+15["Name for Haplotype 2"]@{ shape: lean-l }
+16["Cutadapt"]@{ shape: process }
+0 --> 16
+17["Compute"]@{ shape: process }
+10 --> 17
+18["Search in textfiles"]@{ shape: process }
+11 --> 18
+19["MultiQC"]@{ shape: process }
+16 --> 19
+20["Cut"]@{ shape: process }
+17 --> 20
+21["Replace Text"]@{ shape: process }
+18 --> 21
+22["Parse parameter value"]@{ shape: process }
+20 --> 22
+23["Convert"]@{ shape: process }
+21 --> 23
+24["Homozygous read coverage for Hifiasm"]@{ shape: process }
+9 --> 24
+22 --> 24
+25["Cut"]@{ shape: process }
+23 --> 25
+26["Hifiasm"]@{ shape: process }
+24 --> 26
+6 --> 26
+16 --> 26
+12 --> 26
+1 --> 26
+2 --> 26
+27["Estimated genome size"]@{ shape: process }
+25 --> 27
+28["gfastats"]@{ shape: process }
+26 --> 28
+13 --> 28
+29["gfastats"]@{ shape: process }
+26 --> 29
+13 --> 29
+30["Raw Unitig Image"]@{ shape: process }
+26 --> 30
+31["gfastats"]@{ shape: process }
+26 --> 31
+13 --> 31
+32["gfastats"]@{ shape: process }
+26 --> 32
+13 --> 32
+33["gfastats"]@{ shape: process }
+26 --> 33
+34["gfastats"]@{ shape: process }
+26 --> 34
+35["gfastats"]@{ shape: process }
+26 --> 35
+27 --> 35
+36["gfastats"]@{ shape: process }
+26 --> 36
+27 --> 36
+37["Busco"]@{ shape: process }
+31 --> 37
+7 --> 37
+8 --> 37
+38["Busco"]@{ shape: process }
+32 --> 38
+7 --> 38
+8 --> 38
+39["Merqury"]@{ shape: process }
+31 --> 39
+32 --> 39
+3 --> 39
+5 --> 39
+4 --> 39
+40["Data prep Hap1"]@{ shape: subprocess }
+33 --> 40
+41["Data Prep Hap2"]@{ shape: subprocess }
+34 --> 41
+42["Text reformatting"]@{ shape: process }
+35 --> 42
+43["Text reformatting"]@{ shape: process }
+36 --> 43
+44["merqury_qv"]@{ shape: process }
+39 --> 44
+45["output_merqury.spectra-cn.fl"]@{ shape: process }
+39 --> 45
+46["output_merqury.spectra-asm.fl"]@{ shape: process }
+39 --> 46
+47["output_merqury.assembly_01.spectra-cn.fl"]@{ shape: process }
+39 --> 47
+48["output_merqury.assembly_02.spectra-cn.fl"]@{ shape: process }
+39 --> 48
+49["merqury_stats"]@{ shape: process }
+39 --> 49
+50["Plots"]@{ shape: subprocess }
+41 --> 50
+15 --> 50
+14 --> 50
+40 --> 50
+51["Join two Datasets"]@{ shape: process }
+43 --> 51
+42 --> 51
+52["Advanced Cut"]@{ shape: process }
+51 --> 52
+53["Replace"]@{ shape: process }
+52 --> 53
+```
+
+## gfastats_plot
+
+```mermaid
+graph LR
+0["Primary data"]@{ shape: doc }
+1["Alternate data"]@{ shape: doc }
+2["Name of primary assembly"]@{ shape: lean-l }
+3["Name of alternate assembly"]@{ shape: lean-l }
+4["Add column"]@{ shape: process }
+2 --> 4
+0 --> 4
+5["Add column"]@{ shape: process }
+3 --> 5
+1 --> 5
+6["Concatenate datasets"]@{ shape: process }
+4 --> 6
+5 --> 6
+7["Cut"]@{ shape: process }
+6 --> 7
+8["Cut"]@{ shape: process }
+6 --> 8
+9["Nx Plot"]@{ shape: process }
+7 --> 9
+10["Size Plot"]@{ shape: process }
+8 --> 10
+```
+
+## gfastats_data_prep
+
+```mermaid
+graph LR
+0["gfa_stats"]@{ shape: doc }
+1["Sort"]@{ shape: process }
+0 --> 1
+2["Text reformatting"]@{ shape: process }
+1 --> 2
+3["Datamash"]@{ shape: process }
+2 --> 3
+4["Add column"]@{ shape: process }
+2 --> 4
+5["Parse parameter value"]@{ shape: process }
+3 --> 5
+6["Compose text parameter value"]@{ shape: process }
+5 --> 6
+7["Compute"]@{ shape: process }
+4 --> 7
+6 --> 7
+```
diff --git a/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3_diagrams.md b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3_diagrams.md
new file mode 100644
index 000000000..0da831ca6
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Assembly-Hifi-only-VGP3/Assembly-Hifi-only-VGP3_diagrams.md
@@ -0,0 +1,158 @@
+# Workflow diagrams
+
+## Assembly-Hifi-only-VGP3
+
+```mermaid
+graph LR
+0["Pacbio Reads Collection"]@{ shape: docs }
+1["Meryl Database"]@{ shape: doc }
+2["Genomescope Summary"]@{ shape: doc }
+3["Bits for Hifiasm bloom filter"]@{ shape: lean-l }
+4["Homozygous Read Coverage"]@{ shape: lean-l }
+5["Genomescope Model Parameters"]@{ shape: doc }
+6["Database for Busco Lineage"]@{ shape: lean-l }
+7["Lineage"]@{ shape: lean-l }
+8["SAK input file (Optional)"]@{ shape: doc }
+9["Name of primary assembly"]@{ shape: lean-l }
+10["Name of alternate assembly"]@{ shape: lean-l }
+11["Cutadapt"]@{ shape: process }
+0 --> 11
+12["Search in textfiles"]@{ shape: process }
+2 --> 12
+13["Pick parameter value"]@{ shape: process }
+3 --> 13
+14["Compute"]@{ shape: process }
+5 --> 14
+15["MultiQC"]@{ shape: process }
+11 --> 15
+16["Replace Text"]@{ shape: process }
+12 --> 16
+17["Cut"]@{ shape: process }
+14 --> 17
+18["Convert"]@{ shape: process }
+16 --> 18
+19["Parse parameter value"]@{ shape: process }
+17 --> 19
+20["Cut"]@{ shape: process }
+18 --> 20
+21["Homozygous read coverage for Hifiasm"]@{ shape: process }
+4 --> 21
+19 --> 21
+22["Estimated genome size"]@{ shape: process }
+20 --> 22
+23["Hifiasm"]@{ shape: process }
+21 --> 23
+13 --> 23
+11 --> 23
+24["Raw Unitig Image"]@{ shape: process }
+23 --> 24
+25["gfastats"]@{ shape: process }
+23 --> 25
+8 --> 25
+26["gfastats"]@{ shape: process }
+23 --> 26
+8 --> 26
+27["gfastats"]@{ shape: process }
+23 --> 27
+8 --> 27
+28["gfastats"]@{ shape: process }
+23 --> 28
+8 --> 28
+29["gfastats"]@{ shape: process }
+23 --> 29
+22 --> 29
+30["gfastats"]@{ shape: process }
+23 --> 30
+22 --> 30
+31["gfastats"]@{ shape: process }
+23 --> 31
+32["gfastats"]@{ shape: process }
+23 --> 32
+33["Busco"]@{ shape: process }
+27 --> 33
+6 --> 33
+7 --> 33
+34["Merqury"]@{ shape: process }
+27 --> 34
+28 --> 34
+1 --> 34
+35["Text reformatting"]@{ shape: process }
+29 --> 35
+36["Text reformatting"]@{ shape: process }
+30 --> 36
+37["Data Prep Primary"]@{ shape: subprocess }
+31 --> 37
+38["Data Prep Alternate"]@{ shape: subprocess }
+32 --> 38
+39["merqury_qv"]@{ shape: process }
+34 --> 39
+40["output_merqury.spectra-cn.fl"]@{ shape: process }
+34 --> 40
+41["output_merqury.spectra-asm.fl"]@{ shape: process }
+34 --> 41
+42["output_merqury.assembly_01.spectra-cn.fl"]@{ shape: process }
+34 --> 42
+43["merqury_stats"]@{ shape: process }
+34 --> 43
+44["Join two Datasets"]@{ shape: process }
+35 --> 44
+36 --> 44
+45["Plotting Nx and Sizes"]@{ shape: subprocess }
+38 --> 45
+10 --> 45
+9 --> 45
+37 --> 45
+46["Advanced Cut"]@{ shape: process }
+44 --> 46
+47["Replace"]@{ shape: process }
+46 --> 47
+```
+
+## gfastats_plot
+
+```mermaid
+graph LR
+0["Primary data"]@{ shape: doc }
+1["Alternate data"]@{ shape: doc }
+2["Name of primary assembly"]@{ shape: lean-l }
+3["Name of alternate assembly"]@{ shape: lean-l }
+4["Add column"]@{ shape: process }
+2 --> 4
+0 --> 4
+5["Add column"]@{ shape: process }
+3 --> 5
+1 --> 5
+6["Concatenate datasets"]@{ shape: process }
+4 --> 6
+5 --> 6
+7["Cut"]@{ shape: process }
+6 --> 7
+8["Cut"]@{ shape: process }
+6 --> 8
+9["Nx Plot"]@{ shape: process }
+7 --> 9
+10["Size Plot"]@{ shape: process }
+8 --> 10
+```
+
+## gfastats_data_prep
+
+```mermaid
+graph LR
+0["gfa_stats"]@{ shape: doc }
+1["Sort"]@{ shape: process }
+0 --> 1
+2["Text reformatting"]@{ shape: process }
+1 --> 2
+3["Datamash"]@{ shape: process }
+2 --> 3
+4["Add column"]@{ shape: process }
+2 --> 4
+5["Parse parameter value"]@{ shape: process }
+3 --> 5
+6["Compose text parameter value"]@{ shape: process }
+5 --> 6
+7["Compute"]@{ shape: process }
+4 --> 7
+6 --> 7
+```
diff --git a/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9_diagrams.md b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9_diagrams.md
new file mode 100644
index 000000000..119574e8c
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Assembly-decontamination-VGP9/Assembly-decontamination-VGP9_diagrams.md
@@ -0,0 +1,30 @@
+# Workflow diagrams
+
+## Assembly-decontamination-VGP9
+
+```mermaid
+graph LR
+0["Scaffolded assembly (fasta)"]@{ shape: doc }
+1["Database for Kraken2"]@{ shape: lean-l }
+2["soft-masking "]@{ shape: process }
+0 --> 2
+3["hard-masking"]@{ shape: process }
+2 --> 3
+4["ID non-target contaminants"]@{ shape: process }
+1 --> 4
+3 --> 4
+5["blast mitochondria DB"]@{ shape: process }
+3 --> 5
+6["Cut"]@{ shape: process }
+4 --> 6
+7["parsing blast output"]@{ shape: process }
+5 --> 7
+8["Filter"]@{ shape: process }
+6 --> 8
+9["Cut"]@{ shape: process }
+8 --> 9
+10["concatenate scaffold lists"]@{ shape: process }
+11["removing scaffolds "]@{ shape: process }
+0 --> 11
+10 --> 11
+```
diff --git a/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0_diagrams.md b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0_diagrams.md
new file mode 100644
index 000000000..4e5732e43
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Mitogenome-assembly-VGP0/Mitogenome-Assembly-VGP0_diagrams.md
@@ -0,0 +1,19 @@
+# Workflow diagrams
+
+## Mitogenome-Assembly-VGP0
+
+```mermaid
+graph LR
+0["Collection of Pacbio Data"]@{ shape: docs }
+1["Species name (latin name)"]@{ shape: lean-l }
+2["Email adress"]@{ shape: lean-l }
+3["MitoHiFi"]@{ shape: process }
+2 --> 3
+1 --> 3
+4["MitoHiFi"]@{ shape: process }
+0 --> 4
+3 --> 4
+3 --> 4
+5["Compress file(s)"]@{ shape: process }
+4 --> 5
+```
diff --git a/workflows/VGP-assembly-v2/Plot-Nx-Size/Generate-Nx-and-Size-plots-for-multiple-assemblies_diagrams.md b/workflows/VGP-assembly-v2/Plot-Nx-Size/Generate-Nx-and-Size-plots-for-multiple-assemblies_diagrams.md
new file mode 100644
index 000000000..ca7050670
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Plot-Nx-Size/Generate-Nx-and-Size-plots-for-multiple-assemblies_diagrams.md
@@ -0,0 +1,37 @@
+# Workflow diagrams
+
+## Generate Nx and Size plots for multiple assemblies
+
+```mermaid
+graph LR
+0["Collection of genomes to plot"]@{ shape: docs }
+1["gfastats"]@{ shape: process }
+0 --> 1
+2["Sort"]@{ shape: process }
+1 --> 2
+3["Text reformatting"]@{ shape: process }
+2 --> 3
+4["Datamash"]@{ shape: process }
+3 --> 4
+5["Add column"]@{ shape: process }
+3 --> 5
+6["Parse parameter value"]@{ shape: process }
+4 --> 6
+7["Compose text parameter value"]@{ shape: process }
+6 --> 7
+8["Compute"]@{ shape: process }
+5 --> 8
+7 --> 8
+9["Add input name as column"]@{ shape: process }
+8 --> 9
+10["Collapse Collection"]@{ shape: process }
+9 --> 10
+11["Cut"]@{ shape: process }
+10 --> 11
+12["Cut"]@{ shape: process }
+10 --> 12
+13["Nx Plot"]@{ shape: process }
+11 --> 13
+14["Size Plot"]@{ shape: process }
+12 --> 14
+```
diff --git a/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6_diagrams.md b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6_diagrams.md
new file mode 100644
index 000000000..27094df20
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Purge-duplicate-contigs-VGP6/Purge-duplicate-contigs-VGP6_diagrams.md
@@ -0,0 +1,182 @@
+# Workflow diagrams
+
+## Purge-duplicate-contigs-VGP6
+
+```mermaid
+graph LR
+0["Pacbio Reads Collection - Trimmed"]@{ shape: docs }
+1["Hifiasm Primary assembly"]@{ shape: doc }
+2["Hifiasm Alternate assembly"]@{ shape: doc }
+3["Meryl Database"]@{ shape: doc }
+4["Genomescope model parameters"]@{ shape: doc }
+5["Estimated genome size - Parameter File"]@{ shape: doc }
+6["Database for Busco Lineage"]@{ shape: lean-l }
+7["Lineage"]@{ shape: lean-l }
+8["SAK input file"]@{ shape: doc }
+9["Name of primary assembly"]@{ shape: lean-l }
+10["Name of alternate assembly"]@{ shape: lean-l }
+11["Map with minimap2"]@{ shape: process }
+0 --> 11
+1 --> 11
+12["Purge overlaps"]@{ shape: process }
+1 --> 12
+13["Compute"]@{ shape: process }
+4 --> 13
+14["Estimated genome size"]@{ shape: process }
+5 --> 14
+15["Awk command for primary assembly"]@{ shape: process }
+9 --> 15
+16["Awk command for alternate assembly 2"]@{ shape: process }
+10 --> 16
+17["Map with minimap2"]@{ shape: process }
+12 --> 17
+12 --> 17
+18["Cut"]@{ shape: process }
+13 --> 18
+19["Cut"]@{ shape: process }
+13 --> 19
+20["Parse parameter value"]@{ shape: process }
+18 --> 20
+21["Parse parameter value"]@{ shape: process }
+19 --> 21
+22["Purge overlaps"]@{ shape: process }
+11 --> 22
+21 --> 22
+20 --> 22
+23["Purge overlaps"]@{ shape: process }
+22 --> 23
+22 --> 23
+17 --> 23
+24["Purge overlaps"]@{ shape: process }
+23 --> 24
+1 --> 24
+25["Concatenate datasets"]@{ shape: process }
+24 --> 25
+2 --> 25
+26["Busco"]@{ shape: process }
+24 --> 26
+6 --> 26
+7 --> 26
+27["gfastats"]@{ shape: process }
+24 --> 27
+8 --> 27
+28["gfastats"]@{ shape: process }
+24 --> 28
+14 --> 28
+29["gfastats"]@{ shape: process }
+24 --> 29
+30["Map with minimap2"]@{ shape: process }
+0 --> 30
+25 --> 30
+31["Purge overlaps"]@{ shape: process }
+25 --> 31
+32["Text reformatting"]@{ shape: process }
+15 --> 32
+28 --> 32
+33["gfastats_data_prep"]@{ shape: subprocess }
+29 --> 33
+34["Purge overlaps"]@{ shape: process }
+30 --> 34
+21 --> 34
+20 --> 34
+35["Map with minimap2"]@{ shape: process }
+31 --> 35
+31 --> 35
+36["Purge overlaps"]@{ shape: process }
+34 --> 36
+34 --> 36
+35 --> 36
+37["Purge overlaps"]@{ shape: process }
+36 --> 37
+25 --> 37
+38["gfastats"]@{ shape: process }
+37 --> 38
+14 --> 38
+39["gfastats"]@{ shape: process }
+37 --> 39
+40["Merqury"]@{ shape: process }
+24 --> 40
+37 --> 40
+3 --> 40
+41["gfastats"]@{ shape: process }
+37 --> 41
+8 --> 41
+42["Text reformatting"]@{ shape: process }
+16 --> 42
+38 --> 42
+43["gfastats_data_prep"]@{ shape: subprocess }
+39 --> 43
+44["merqury_QV"]@{ shape: process }
+40 --> 44
+45["output_merqury.spectra-cn.fl"]@{ shape: process }
+40 --> 45
+46["output_merqury.spectra-asm.fl"]@{ shape: process }
+40 --> 46
+47["output_merqury.assembly_01.spectra-cn.fl"]@{ shape: process }
+40 --> 47
+48["merqury_stats"]@{ shape: process }
+40 --> 48
+49["output_merqury.assembly_02.spectra-cn.fl"]@{ shape: process }
+40 --> 49
+50["Join two Datasets"]@{ shape: process }
+32 --> 50
+42 --> 50
+51["gfastats_plot"]@{ shape: subprocess }
+43 --> 51
+10 --> 51
+9 --> 51
+33 --> 51
+52["Advanced Cut"]@{ shape: process }
+50 --> 52
+53["Replace"]@{ shape: process }
+52 --> 53
+```
+
+## gfastats_plot
+
+```mermaid
+graph LR
+0["Primary data"]@{ shape: doc }
+1["Alternate data"]@{ shape: doc }
+2["Name of primary assembly"]@{ shape: lean-l }
+3["Name of alternate assembly"]@{ shape: lean-l }
+4["Add column"]@{ shape: process }
+2 --> 4
+0 --> 4
+5["Add column"]@{ shape: process }
+3 --> 5
+1 --> 5
+6["Concatenate datasets"]@{ shape: process }
+4 --> 6
+5 --> 6
+7["Cut"]@{ shape: process }
+6 --> 7
+8["Cut"]@{ shape: process }
+6 --> 8
+9["Nx Plot"]@{ shape: process }
+7 --> 9
+10["Size Plot"]@{ shape: process }
+8 --> 10
+```
+
+## gfastats_data_prep
+
+```mermaid
+graph LR
+0["gfa_stats"]@{ shape: doc }
+1["Sort"]@{ shape: process }
+0 --> 1
+2["Text reformatting"]@{ shape: process }
+1 --> 2
+3["Datamash"]@{ shape: process }
+2 --> 3
+4["Add column"]@{ shape: process }
+2 --> 4
+5["Parse parameter value"]@{ shape: process }
+3 --> 5
+6["Compose text parameter value"]@{ shape: process }
+5 --> 6
+7["Compute"]@{ shape: process }
+4 --> 7
+6 --> 7
+```
diff --git a/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b_diagrams.md b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b_diagrams.md
new file mode 100644
index 000000000..eb2bbf03c
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Purge-duplicates-one-haplotype-VGP6b/Purging-duplicates-one-haplotype-VGP6b_diagrams.md
@@ -0,0 +1,151 @@
+# Workflow diagrams
+
+## Purging-duplicates-one-haplotype-VGP6b 
+
+```mermaid
+graph LR
+0["Genomescope model parameters"]@{ shape: doc }
+1["Pacbio Reads Collection - Trimmed"]@{ shape: docs }
+2["Assembly to purge"]@{ shape: doc }
+3["Meryl Database"]@{ shape: doc }
+4["Assembly to leave alone (For Merqury comparison)"]@{ shape: doc }
+5["Estimated genome size - Parameter File"]@{ shape: doc }
+6["Database for Busco Lineage"]@{ shape: lean-l }
+7["Lineage"]@{ shape: lean-l }
+8["Name of purged assembly"]@{ shape: lean-l }
+9["Name of un-altered assembly"]@{ shape: lean-l }
+10["Compute"]@{ shape: process }
+0 --> 10
+11["Map with minimap2"]@{ shape: process }
+1 --> 11
+2 --> 11
+12["Purge overlaps"]@{ shape: process }
+2 --> 12
+13["gfastats"]@{ shape: process }
+4 --> 13
+14["Estimated genome size"]@{ shape: process }
+5 --> 14
+15["Cut"]@{ shape: process }
+10 --> 15
+16["Cut"]@{ shape: process }
+10 --> 16
+17["Map with minimap2"]@{ shape: process }
+12 --> 17
+12 --> 17
+18["gfastats_data_prep"]@{ shape: subprocess }
+13 --> 18
+19["gfastats"]@{ shape: process }
+4 --> 19
+14 --> 19
+20["Parse parameter value"]@{ shape: process }
+15 --> 20
+21["Parse parameter value"]@{ shape: process }
+16 --> 21
+22["Text reformatting"]@{ shape: process }
+19 --> 22
+23["Purge overlaps"]@{ shape: process }
+11 --> 23
+21 --> 23
+20 --> 23
+24["Purge overlaps"]@{ shape: process }
+23 --> 24
+23 --> 24
+17 --> 24
+25["Remove REPEATs from BED"]@{ shape: process }
+24 --> 25
+26["Purge overlaps"]@{ shape: process }
+25 --> 26
+2 --> 26
+27["Merqury"]@{ shape: process }
+26 --> 27
+4 --> 27
+3 --> 27
+28["gfastats"]@{ shape: process }
+26 --> 28
+29["Busco"]@{ shape: process }
+26 --> 29
+6 --> 29
+7 --> 29
+30["Convert purged fasta to gfa"]@{ shape: process }
+26 --> 30
+31["gfastats"]@{ shape: process }
+26 --> 31
+14 --> 31
+32["merqury_QV"]@{ shape: process }
+27 --> 32
+33["output_merqury.spectra-cn.fl"]@{ shape: process }
+27 --> 33
+34["output_merqury.spectra-asm.fl"]@{ shape: process }
+27 --> 34
+35["output_merqury.assembly_01.spectra-cn.fl"]@{ shape: process }
+27 --> 35
+36["merqury_stats"]@{ shape: process }
+27 --> 36
+37["output_merqury.assembly_02.spectra-cn.fl"]@{ shape: process }
+27 --> 37
+38["gfastats_data_prep"]@{ shape: subprocess }
+28 --> 38
+39["Text reformatting"]@{ shape: process }
+31 --> 39
+40["gfastats_plot"]@{ shape: subprocess }
+18 --> 40
+9 --> 40
+8 --> 40
+38 --> 40
+41["Join two Datasets"]@{ shape: process }
+39 --> 41
+22 --> 41
+42["Advanced Cut"]@{ shape: process }
+41 --> 42
+43["Replace"]@{ shape: process }
+42 --> 43
+```
+
+## gfastats_plot
+
+```mermaid
+graph LR
+0["Primary data"]@{ shape: doc }
+1["Alternate data"]@{ shape: doc }
+2["Name of primary assembly"]@{ shape: lean-l }
+3["Name of alternate assembly"]@{ shape: lean-l }
+4["Add column"]@{ shape: process }
+2 --> 4
+0 --> 4
+5["Add column"]@{ shape: process }
+3 --> 5
+1 --> 5
+6["Concatenate datasets"]@{ shape: process }
+4 --> 6
+5 --> 6
+7["Cut"]@{ shape: process }
+6 --> 7
+8["Cut"]@{ shape: process }
+6 --> 8
+9["Nx Plot"]@{ shape: process }
+7 --> 9
+10["Size Plot"]@{ shape: process }
+8 --> 10
+```
+
+## gfastats_data_prep
+
+```mermaid
+graph LR
+0["gfa_stats"]@{ shape: doc }
+1["Sort"]@{ shape: process }
+0 --> 1
+2["Text reformatting"]@{ shape: process }
+1 --> 2
+3["Datamash"]@{ shape: process }
+2 --> 3
+4["Add column"]@{ shape: process }
+2 --> 4
+5["Parse parameter value"]@{ shape: process }
+3 --> 5
+6["Compose text parameter value"]@{ shape: process }
+5 --> 6
+7["Compute"]@{ shape: process }
+4 --> 7
+6 --> 7
+```
diff --git a/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7_diagrams.md b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7_diagrams.md
new file mode 100644
index 000000000..1377ae4b4
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Scaffolding-Bionano-VGP7/Scaffolding-BioNano-VGP7_diagrams.md
@@ -0,0 +1,63 @@
+# Workflow diagrams
+
+## Scaffolding-BioNano-VGP7
+
+```mermaid
+graph LR
+0["Bionano Data"]@{ shape: doc }
+1["Estimated genome size - Parameter File"]@{ shape: doc }
+2["Input GFA"]@{ shape: doc }
+3["Conflict resolution files"]@{ shape: doc }
+4["Parse parameter value"]@{ shape: process }
+1 --> 4
+5["gfastats"]@{ shape: process }
+2 --> 5
+6["Bionano Hybrid Scaffold"]@{ shape: process }
+0 --> 6
+3 --> 6
+5 --> 6
+7["gfastats"]@{ shape: process }
+2 --> 7
+6 --> 7
+8["gfastats"]@{ shape: process }
+7 --> 8
+9["gfastats"]@{ shape: process }
+7 --> 9
+4 --> 9
+10["gfastats"]@{ shape: process }
+7 --> 10
+11["Replace"]@{ shape: process }
+9 --> 11
+12["gfastats_data_prep"]@{ shape: subprocess }
+10 --> 12
+13["Cut"]@{ shape: process }
+12 --> 13
+14["Cut"]@{ shape: process }
+12 --> 14
+15["Scatterplot with ggplot2"]@{ shape: process }
+13 --> 15
+16["Scatterplot with ggplot2"]@{ shape: process }
+14 --> 16
+```
+
+## gfastats_data_prep
+
+```mermaid
+graph LR
+0["gfa_stats"]@{ shape: doc }
+1["Sort"]@{ shape: process }
+0 --> 1
+2["Text reformatting"]@{ shape: process }
+1 --> 2
+3["Datamash"]@{ shape: process }
+2 --> 3
+4["Add column"]@{ shape: process }
+2 --> 4
+5["Parse parameter value"]@{ shape: process }
+3 --> 5
+6["Compose text parameter value"]@{ shape: process }
+5 --> 6
+7["Compute"]@{ shape: process }
+4 --> 7
+6 --> 7
+```
diff --git a/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8_diagrams.md b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8_diagrams.md
new file mode 100644
index 000000000..e045479f4
--- /dev/null
+++ b/workflows/VGP-assembly-v2/Scaffolding-HiC-VGP8/Scaffolding-HiC-VGP8_diagrams.md
@@ -0,0 +1,115 @@
+# Workflow diagrams
+
+## Scaffolding with Hi-C data VGP8
+
+```mermaid
+graph LR
+0["Input GFA"]@{ shape: doc }
+1["Haplotype"]@{ shape: lean-l }
+2["Sequence graph"]@{ shape: doc }
+3["Database for Busco Lineage"]@{ shape: lean-l }
+4["Lineage"]@{ shape: lean-l }
+5["HiC Forward reads"]@{ shape: doc }
+6["HiC reverse reads"]@{ shape: doc }
+7["Restriction enzymes"]@{ shape: lean-l }
+8["Estimated genome size - Parameter File"]@{ shape: doc }
+9["SAK input file"]@{ shape: doc }
+10["Compose text parameter value"]@{ shape: process }
+1 --> 10
+11["Parse parameter value"]@{ shape: process }
+8 --> 11
+12["gfastats"]@{ shape: process }
+0 --> 12
+9 --> 12
+13["BWA-MEM2"]@{ shape: process }
+5 --> 13
+12 --> 13
+14["BWA-MEM2"]@{ shape: process }
+6 --> 14
+12 --> 14
+15["Filter and merge"]@{ shape: process }
+13 --> 15
+14 --> 15
+16["PretextMap"]@{ shape: process }
+15 --> 16
+17["YAHS"]@{ shape: process }
+2 --> 17
+15 --> 17
+7 --> 17
+12 --> 17
+18["Pretext Snapshot"]@{ shape: process }
+16 --> 18
+19["Replace"]@{ shape: process }
+10 --> 19
+17 --> 19
+20["Extract dataset"]@{ shape: process }
+18 --> 20
+21["gfastats"]@{ shape: process }
+12 --> 21
+19 --> 21
+22["gfastats"]@{ shape: process }
+21 --> 22
+9 --> 22
+23["gfastats"]@{ shape: process }
+21 --> 23
+11 --> 23
+24["gfastats"]@{ shape: process }
+21 --> 24
+25["BWA-MEM2"]@{ shape: process }
+5 --> 25
+22 --> 25
+26["BWA-MEM2"]@{ shape: process }
+6 --> 26
+22 --> 26
+27["Busco"]@{ shape: process }
+22 --> 27
+3 --> 27
+4 --> 27
+28["Replace"]@{ shape: process }
+23 --> 28
+29["gfastats_data_prep"]@{ shape: subprocess }
+24 --> 29
+30["Filter and merge"]@{ shape: process }
+25 --> 30
+26 --> 30
+31["Cut"]@{ shape: process }
+29 --> 31
+32["Cut"]@{ shape: process }
+29 --> 32
+33["PretextMap"]@{ shape: process }
+30 --> 33
+34["bedtools BAM to BED"]@{ shape: process }
+30 --> 34
+35["Nx Plot"]@{ shape: process }
+31 --> 35
+36["Size Plot"]@{ shape: process }
+32 --> 36
+37["Pretext Snapshot"]@{ shape: process }
+33 --> 37
+38["Sort"]@{ shape: process }
+34 --> 38
+39["Extract dataset"]@{ shape: process }
+37 --> 39
+```
+
+## gfastats_data_prep
+
+```mermaid
+graph LR
+0["gfa_stats"]@{ shape: doc }
+1["Sort"]@{ shape: process }
+0 --> 1
+2["Text reformatting"]@{ shape: process }
+1 --> 2
+3["Datamash"]@{ shape: process }
+2 --> 3
+4["Add column"]@{ shape: process }
+2 --> 4
+5["Parse parameter value"]@{ shape: process }
+3 --> 5
+6["Compose text parameter value"]@{ shape: process }
+5 --> 6
+7["Compute"]@{ shape: process }
+4 --> 7
+6 --> 7
+```
diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1_diagrams.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1_diagrams.md
new file mode 100644
index 000000000..0e5871490
--- /dev/null
+++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-VGP1/kmer-profiling-hifi-VGP1_diagrams.md
@@ -0,0 +1,21 @@
+# Workflow diagrams
+
+## kmer-profiling-hifi-VGP1
+
+```mermaid
+graph LR
+0["Collection of Pacbio Data"]@{ shape: docs }
+1["K-mer length "]@{ shape: lean-l }
+2["Ploidy"]@{ shape: lean-l }
+3["Meryl"]@{ shape: process }
+0 --> 3
+1 --> 3
+4["Meryl"]@{ shape: process }
+3 --> 4
+5["Meryl"]@{ shape: process }
+4 --> 5
+6["GenomeScope"]@{ shape: process }
+5 --> 6
+1 --> 6
+2 --> 6
+```
diff --git a/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2_diagrams.md b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2_diagrams.md
new file mode 100644
index 000000000..6defb9886
--- /dev/null
+++ b/workflows/VGP-assembly-v2/kmer-profiling-hifi-trio-VGP2/kmer-profiling-hifi-trio-VGP2_diagrams.md
@@ -0,0 +1,43 @@
+# Workflow diagrams
+
+## kmer-profiling-hifi-trio-VGP2
+
+```mermaid
+graph LR
+0["Pacbio Hifi reads"]@{ shape: docs }
+1["Paternal reads"]@{ shape: docs }
+2["Maternal reads"]@{ shape: docs }
+3["K-mer length"]@{ shape: lean-l }
+4["Ploidy"]@{ shape: lean-l }
+5["Meryl"]@{ shape: process }
+1 --> 5
+3 --> 5
+6["Meryl"]@{ shape: process }
+0 --> 6
+2 --> 6
+3 --> 6
+1 --> 6
+7["Meryl"]@{ shape: process }
+2 --> 7
+3 --> 7
+8["Meryl"]@{ shape: process }
+5 --> 8
+9["GenomeScope"]@{ shape: process }
+6 --> 9
+3 --> 9
+4 --> 9
+10["Meryl"]@{ shape: process }
+7 --> 10
+11["Meryl"]@{ shape: process }
+8 --> 11
+12["Meryl"]@{ shape: process }
+10 --> 12
+13["Genomescope on paternal haplotype"]@{ shape: process }
+11 --> 13
+3 --> 13
+4 --> 13
+14["Genomescope on maternal haplotype"]@{ shape: process }
+12 --> 14
+3 --> 14
+4 --> 14
+```
diff --git a/workflows/amplicon/dada2/dada2_paired_diagrams.md b/workflows/amplicon/dada2/dada2_paired_diagrams.md
new file mode 100644
index 000000000..25fc537b0
--- /dev/null
+++ b/workflows/amplicon/dada2/dada2_paired_diagrams.md
@@ -0,0 +1,55 @@
+# Workflow diagrams
+
+## dada2 amplicon analysis pipeline - for paired end data
+
+```mermaid
+graph LR
+0["Paired input data"]@{ shape: docs }
+1["Read length forward read"]@{ shape: lean-l }
+2["Read length reverse read"]@{ shape: lean-l }
+3["Pool samples"]@{ shape: lean-l }
+4["Cached reference database"]@{ shape: lean-l }
+5["Sort samples"]@{ shape: process }
+0 --> 5
+6["QualityProfile before filterAndTrim"]@{ shape: process }
+5 --> 6
+7["dada2: filterAndTrim"]@{ shape: process }
+5 --> 7
+2 --> 7
+1 --> 7
+8["QualityProfile after filterAndTrim"]@{ shape: process }
+7 --> 8
+9["Unzip collection"]@{ shape: process }
+7 --> 9
+10["dada2: learnErrors"]@{ shape: process }
+9 --> 10
+11["dada2: learnErrors"]@{ shape: process }
+9 --> 11
+12["dada2: dada"]@{ shape: process }
+9 --> 12
+3 --> 12
+10 --> 12
+13["dada2: dada"]@{ shape: process }
+9 --> 13
+3 --> 13
+11 --> 13
+14["dada2: mergePairs"]@{ shape: process }
+12 --> 14
+13 --> 14
+9 --> 14
+9 --> 14
+15["dada2: makeSequenceTable"]@{ shape: process }
+14 --> 15
+16["dada2: removeBimeraDenovo"]@{ shape: process }
+15 --> 16
+17["dada2: sequence counts"]@{ shape: process }
+7 --> 17
+12 --> 17
+13 --> 17
+14 --> 17
+15 --> 17
+16 --> 17
+18["dada2: assignTaxonomy"]@{ shape: process }
+4 --> 18
+16 --> 18
+```
diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end_diagrams.md b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end_diagrams.md
new file mode 100644
index 000000000..3d80f0ae9
--- /dev/null
+++ b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ia-multiplexed-data-single-end_diagrams.md
@@ -0,0 +1,24 @@
+# Workflow diagrams
+
+## QIIME2 Ia: multiplexed data (single-end)
+
+```mermaid
+graph LR
+0["Sequences"]@{ shape: doc }
+1["Barcodes"]@{ shape: doc }
+2["Metadata"]@{ shape: doc }
+3["Metadata parameter"]@{ shape: lean-l }
+4["Reverse complement barcodes"]@{ shape: lean-l }
+5["Input files"]@{ shape: process }
+1 --> 5
+0 --> 5
+6["Metadata as artifact"]@{ shape: process }
+2 --> 6
+7["Demultiplex single-end data"]@{ shape: process }
+4 --> 7
+3 --> 7
+6 --> 7
+5 --> 7
+8["Summarize demultiplexed output"]@{ shape: process }
+7 --> 8
+```
diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end_diagrams.md b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end_diagrams.md
new file mode 100644
index 000000000..9bb7803a8
--- /dev/null
+++ b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ib-multiplexed-data-paired-end_diagrams.md
@@ -0,0 +1,26 @@
+# Workflow diagrams
+
+## QIIME2 Ib: multiplexed data (paired-end)
+
+```mermaid
+graph LR
+0["Forward sequences"]@{ shape: doc }
+1["Reverse sequences"]@{ shape: doc }
+2["Barcodes"]@{ shape: doc }
+3["Metadata"]@{ shape: doc }
+4["Metadata parameter"]@{ shape: lean-l }
+5["Reverse complement of barcodes needed?"]@{ shape: lean-l }
+6["Import data into the pipeline"]@{ shape: process }
+2 --> 6
+0 --> 6
+1 --> 6
+7["Metadata as artifact"]@{ shape: process }
+3 --> 7
+8["Demultiplex paired-end sequences"]@{ shape: process }
+5 --> 8
+4 --> 8
+7 --> 8
+6 --> 8
+9["Summarising the demultiplexed output"]@{ shape: process }
+8 --> 9
+```
diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ic-demultiplexed-data-single-end_diagrams.md b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ic-demultiplexed-data-single-end_diagrams.md
new file mode 100644
index 000000000..59b51d60b
--- /dev/null
+++ b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Ic-demultiplexed-data-single-end_diagrams.md
@@ -0,0 +1,19 @@
+# Workflow diagrams
+
+## QIIME2 Ic: Demultiplexed data (single-end)
+
+```mermaid
+graph LR
+0["Sequence collection"]@{ shape: docs }
+1["Extract element identifiers"]@{ shape: process }
+0 --> 1
+2["Screening laneless and single-lane"]@{ shape: process }
+1 --> 2
+3["Relabel sequence files"]@{ shape: process }
+2 --> 3
+0 --> 3
+4["Import data into the pipeline"]@{ shape: process }
+3 --> 4
+5["Summarising the demultiplexed output"]@{ shape: process }
+4 --> 5
+```
diff --git a/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end_diagrams.md b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end_diagrams.md
new file mode 100644
index 000000000..8494de800
--- /dev/null
+++ b/workflows/amplicon/qiime2/qiime2-I-import/QIIME2-Id-demultiplexed-data-paired-end_diagrams.md
@@ -0,0 +1,19 @@
+# Workflow diagrams
+
+## QIIME2 Id: Demultiplexed data (paired-end)
+
+```mermaid
+graph LR
+0["Sequence collection"]@{ shape: docs }
+1["Extract element identifiers"]@{ shape: process }
+0 --> 1
+2["Screening laneless and single-lane"]@{ shape: process }
+1 --> 2
+3["Relabel sequence files"]@{ shape: process }
+2 --> 3
+0 --> 3
+4["Import data into the pipeline"]@{ shape: process }
+3 --> 4
+5["Summarising the demultiplexed output"]@{ shape: process }
+4 --> 5
+```
diff --git a/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end_diagrams.md b/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end_diagrams.md
new file mode 100644
index 000000000..dc46e4b23
--- /dev/null
+++ b/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIa-denoising-and-feature-table-creation-single-end_diagrams.md
@@ -0,0 +1,22 @@
+# Workflow diagrams
+
+## QIIME2 IIa: Denoising (sequence quality control) and feature table creation (single-end)
+
+```mermaid
+graph LR
+0["Metadata"]@{ shape: doc }
+1["Demultiplexed sequences"]@{ shape: doc }
+2["Truncation length"]@{ shape: lean-l }
+3["Trimming length"]@{ shape: lean-l }
+4["Denoising the datasets"]@{ shape: process }
+3 --> 4
+1 --> 4
+2 --> 4
+5["Tabulate DADA2 denoised representative sequences"]@{ shape: process }
+4 --> 5
+6["Tabulate DADA2 statistical metadata "]@{ shape: process }
+4 --> 6
+7["Summing up the dada2 output table"]@{ shape: process }
+0 --> 7
+4 --> 7
+```
diff --git a/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end_diagrams.md b/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end_diagrams.md
new file mode 100644
index 000000000..a60a854c3
--- /dev/null
+++ b/workflows/amplicon/qiime2/qiime2-II-denoising/QIIME2-IIb-denoising-and-feature-table-creation-paired-end_diagrams.md
@@ -0,0 +1,26 @@
+# Workflow diagrams
+
+## QIIME2 IIb: Denoising (sequence quality control) and feature table creation (paired-end)
+
+```mermaid
+graph LR
+0["Metadata"]@{ shape: doc }
+1["Demultiplexed sequences"]@{ shape: doc }
+2["Truncation length (forward)"]@{ shape: lean-l }
+3["Truncation length (reverse)"]@{ shape: lean-l }
+4["Trimming length (forward)"]@{ shape: lean-l }
+5["Trimming length (reverse)"]@{ shape: lean-l }
+6["Denoising the datasets"]@{ shape: process }
+4 --> 6
+5 --> 6
+1 --> 6
+2 --> 6
+3 --> 6
+7["Tabulate DADA2 denoised representative sequences"]@{ shape: process }
+6 --> 7
+8["Tabulate DADA2 statistical metadata "]@{ shape: process }
+6 --> 8
+9["Summing up the dada2 output table"]@{ shape: process }
+0 --> 9
+6 --> 9
+```
diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis_diagrams.md b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis_diagrams.md
new file mode 100644
index 000000000..2a14f9b29
--- /dev/null
+++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis_diagrams.md
@@ -0,0 +1,75 @@
+# Workflow diagrams
+
+## QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis
+
+```mermaid
+graph LR
+0["Representative sequences"]@{ shape: doc }
+1["Feature table"]@{ shape: doc }
+2["Metadata"]@{ shape: doc }
+3["Minimum depth"]@{ shape: lean-l }
+4["Maximum depth"]@{ shape: lean-l }
+5["SEPP fragment insertion reference"]@{ shape: doc }
+6["Taxonomic classifier"]@{ shape: doc }
+7["Phylogenetic tree for diversity analysis"]@{ shape: subprocess }
+0 --> 7
+5 --> 7
+8["Taxonomic analysis"]@{ shape: subprocess }
+1 --> 8
+0 --> 8
+2 --> 8
+6 --> 8
+9["Rarefaction"]@{ shape: subprocess }
+1 --> 9
+4 --> 9
+2 --> 9
+3 --> 9
+7 --> 9
+```
+
+## QIIME2 IV: Rarefaction
+
+```mermaid
+graph LR
+0["Metadata"]@{ shape: doc }
+1["DADA2 feature table"]@{ shape: doc }
+2["Rooted tree"]@{ shape: doc }
+3["Minimum depth"]@{ shape: lean-l }
+4["Maximum depth"]@{ shape: lean-l }
+5["Alpha rarefaction"]@{ shape: process }
+0 --> 5
+3 --> 5
+2 --> 5
+4 --> 5
+1 --> 5
+```
+
+## QIIME2 V: Taxonomic analysis
+
+```mermaid
+graph LR
+0["Metadata"]@{ shape: doc }
+1["DADA2 representative sequences"]@{ shape: doc }
+2["Taxonomic classifier"]@{ shape: doc }
+3["DADA2 feature table"]@{ shape: doc }
+4["Taxonomy classification"]@{ shape: process }
+2 --> 4
+1 --> 4
+5["Taxonomy barplot"]@{ shape: process }
+0 --> 5
+4 --> 5
+3 --> 5
+6["Tabulate taxonomy classification"]@{ shape: process }
+4 --> 6
+```
+
+## QIIME2 III: Phylogenetic tree for diversity analysis
+
+```mermaid
+graph LR
+0["DADA2 representative sequences"]@{ shape: doc }
+1["SEPP fragment insertion source file"]@{ shape: doc }
+2["Phylogenetic tree generation"]@{ shape: process }
+1 --> 2
+0 --> 2
+```
diff --git a/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations_diagrams.md b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations_diagrams.md
new file mode 100644
index 000000000..4a86fd2c6
--- /dev/null
+++ b/workflows/amplicon/qiime2/qiime2-III-VI-downsteam/QIIME2-VI-diversity-metrics-and-estimations_diagrams.md
@@ -0,0 +1,61 @@
+# Workflow diagrams
+
+## QIIME2 VI: Diversity metrics and estimations
+
+```mermaid
+graph LR
+0["Sampling depth"]@{ shape: lean-l }
+1["Metadata"]@{ shape: doc }
+2["Feature table"]@{ shape: doc }
+3["Rooted tree"]@{ shape: doc }
+4["Target metadata parameter (for beta diversity)"]@{ shape: lean-l }
+5["qiime2 tools import"]@{ shape: process }
+1 --> 5
+6["Diversity metrics"]@{ shape: process }
+1 --> 6
+3 --> 6
+0 --> 6
+2 --> 6
+7["Alpha diversity metrics - Pielou's evenness"]@{ shape: process }
+6 --> 7
+1 --> 7
+8["Alpha diversity metrics - Observed features"]@{ shape: process }
+6 --> 8
+1 --> 8
+9["Alpha diversity metrics - Shannon's diversity index"]@{ shape: process }
+6 --> 9
+1 --> 9
+10["Beta diversity - Jaccard distance matrix"]@{ shape: process }
+6 --> 10
+4 --> 10
+5 --> 10
+11["Beta diversity - Bray-Curtis distance matrix"]@{ shape: process }
+6 --> 11
+4 --> 11
+5 --> 11
+12["Emperor plot collection"]@{ shape: process }
+6 --> 12
+6 --> 12
+6 --> 12
+6 --> 12
+13["Beta diversity - weighted UniFrac distance matrix"]@{ shape: process }
+6 --> 13
+4 --> 13
+5 --> 13
+14["PCoA collection"]@{ shape: process }
+6 --> 14
+6 --> 14
+6 --> 14
+6 --> 14
+15["Distance matrix collection"]@{ shape: process }
+6 --> 15
+6 --> 15
+6 --> 15
+6 --> 15
+16["Richness and evenness collection"]@{ shape: process }
+6 --> 16
+6 --> 16
+6 --> 16
+6 --> 16
+6 --> 16
+```
diff --git a/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection_diagrams.md b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection_diagrams.md
new file mode 100644
index 000000000..243c01a77
--- /dev/null
+++ b/workflows/bacterial_genomics/amr_gene_detection/amr_gene_detection_diagrams.md
@@ -0,0 +1,32 @@
+# Workflow diagrams
+
+## amr_gene_detection
+
+```mermaid
+graph LR
+0["Input sequence fasta"]@{ shape: doc }
+1["Select a taxonomy group point mutation"]@{ shape: lean-l }
+2["Select a AMR genes detection database"]@{ shape: lean-l }
+3["Select a virulence genes detection database"]@{ shape: lean-l }
+4["staramr_amr_genes"]@{ shape: process }
+0 --> 4
+5["amrfinderplus_point_mutation"]@{ shape: process }
+2 --> 5
+0 --> 5
+1 --> 5
+6["abricate_virulence"]@{ shape: process }
+3 --> 6
+0 --> 6
+7["ToolDistillator"]@{ shape: process }
+6 --> 7
+3 --> 7
+4 --> 7
+4 --> 7
+4 --> 7
+5 --> 7
+5 --> 7
+5 --> 7
+2 --> 7
+8["ToolDistillator summarize"]@{ shape: process }
+7 --> 8
+```
diff --git a/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation_diagrams.md b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation_diagrams.md
new file mode 100644
index 000000000..02e161286
--- /dev/null
+++ b/workflows/bacterial_genomics/bacterial_genome_annotation/bacterial_genome_annotation_diagrams.md
@@ -0,0 +1,51 @@
+# Workflow diagrams
+
+## bacterial_genome_annotation
+
+```mermaid
+graph LR
+0["Input sequence fasta"]@{ shape: doc }
+1["Select a plasmid detection database"]@{ shape: lean-l }
+2["Select a bacterial genome annotation database"]@{ shape: lean-l }
+3["Select a AMRFinderPlus database"]@{ shape: lean-l }
+4["genomic_annotation_insertionelement_isescan"]@{ shape: process }
+0 --> 4
+5["genomic_annotation_integron"]@{ shape: process }
+0 --> 5
+6["genomic_annotation_plasmid_plasmidfinder"]@{ shape: process }
+1 --> 6
+0 --> 6
+7["Bakta"]@{ shape: process }
+3 --> 7
+2 --> 7
+0 --> 7
+8["ToolDistillator"]@{ shape: process }
+6 --> 8
+6 --> 8
+6 --> 8
+6 --> 8
+1 --> 8
+4 --> 8
+4 --> 8
+4 --> 8
+4 --> 8
+4 --> 8
+4 --> 8
+5 --> 8
+5 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+2 --> 8
+7 --> 8
+9["ToolDistillator summarize"]@{ shape: process }
+8 --> 9
+```
diff --git a/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring_diagrams.md b/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring_diagrams.md
new file mode 100644
index 000000000..9d68316a6
--- /dev/null
+++ b/workflows/computational-chemistry/fragment-based-docking-scoring/fragment-based-docking-scoring_diagrams.md
@@ -0,0 +1,43 @@
+# Workflow diagrams
+
+## Fragment-based virtual screening using rDock for docking and SuCOS for pose scoring
+
+```mermaid
+graph LR
+0["Number of poses"]@{ shape: lean-l }
+1["Receptor (PDB)"]@{ shape: doc }
+2["All fragments (SDF)"]@{ shape: doc }
+3["Collection size for docking"]@{ shape: lean-l }
+4["SuCOS threshold"]@{ shape: lean-l }
+5["Fragment for SuCOS scoring (SDF/MOL)"]@{ shape: doc }
+6["Candidate compounds (SMILES)"]@{ shape: doc }
+7["Compound conversion"]@{ shape: process }
+1 --> 7
+8["Create Frankenstein ligand"]@{ shape: process }
+2 --> 8
+9["Compose text parameter value"]@{ shape: process }
+4 --> 9
+10["Enumerate changes"]@{ shape: process }
+6 --> 10
+11["rDock cavity definition"]@{ shape: process }
+8 --> 11
+7 --> 11
+12["Compound conversion"]@{ shape: process }
+10 --> 12
+13["Split file"]@{ shape: process }
+12 --> 13
+3 --> 13
+14["rDock docking"]@{ shape: process }
+11 --> 14
+13 --> 14
+0 --> 14
+7 --> 14
+15["Collapse Collection"]@{ shape: process }
+14 --> 15
+16["Score docked poses using SuCOS"]@{ shape: process }
+15 --> 16
+5 --> 16
+17["rDock docking"]@{ shape: process }
+9 --> 17
+16 --> 17
+```
diff --git a/workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd_diagrams.md b/workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd_diagrams.md
new file mode 100644
index 000000000..793718508
--- /dev/null
+++ b/workflows/computational-chemistry/gromacs-dctmd/gromacs-dctmd_diagrams.md
@@ -0,0 +1,124 @@
+# Workflow diagrams
+
+## dcTMD calculations with GROMACS
+
+```mermaid
+graph LR
+0["Ligand SDF"]@{ shape: doc }
+1["pH to protonate ligand"]@{ shape: lean-l }
+2["Protein PDB"]@{ shape: doc }
+3["Salt concentration"]@{ shape: lean-l }
+4["Water model"]@{ shape: lean-l }
+5["Force field"]@{ shape: lean-l }
+6["Number of simulations"]@{ shape: lean-l }
+7["Temperature"]@{ shape: lean-l }
+8["Number of equilibration steps"]@{ shape: lean-l }
+9["Online data"]@{ shape: process }
+10["Pulling rate"]@{ shape: lean-l }
+11["Step length (ps)"]@{ shape: lean-l }
+12["Protein pull group"]@{ shape: lean-l }
+13["Number of steps"]@{ shape: lean-l }
+14["Pull group pbcatom"]@{ shape: lean-l }
+15["Create GRO and TOP complex files"]@{ shape: subprocess }
+2 --> 15
+5 --> 15
+0 --> 15
+4 --> 15
+1 --> 15
+16["Create text file"]@{ shape: process }
+7 --> 16
+6 --> 16
+17["Compose text parameter value"]@{ shape: process }
+10 --> 17
+18["Compose text parameter value"]@{ shape: process }
+11 --> 18
+19["Compose text parameter value"]@{ shape: process }
+13 --> 19
+20["Compose text parameter value"]@{ shape: process }
+14 --> 20
+21["GROMACS solvation and adding ions"]@{ shape: process }
+3 --> 21
+15 --> 21
+15 --> 21
+22["Split file"]@{ shape: process }
+16 --> 22
+23["Add line to file"]@{ shape: process }
+9 --> 23
+17 --> 23
+24["GROMACS energy minimization"]@{ shape: process }
+21 --> 24
+21 --> 24
+25["Parse parameter value"]@{ shape: process }
+22 --> 25
+26["Add line to file"]@{ shape: process }
+23 --> 26
+19 --> 26
+27["Create GROMACS index files"]@{ shape: process }
+24 --> 27
+28["GROMACS simulation"]@{ shape: process }
+24 --> 28
+15 --> 28
+8 --> 28
+11 --> 28
+25 --> 28
+21 --> 28
+29["Add line to file"]@{ shape: process }
+26 --> 29
+18 --> 29
+30["Text transformation"]@{ shape: process }
+27 --> 30
+31["Add line to file"]@{ shape: process }
+29 --> 31
+20 --> 31
+32["Add line to file"]@{ shape: process }
+30 --> 32
+12 --> 32
+33["Concatenate datasets"]@{ shape: process }
+27 --> 33
+32 --> 33
+34["GROMACS simulation"]@{ shape: process }
+28 --> 34
+28 --> 34
+33 --> 34
+31 --> 34
+21 --> 34
+35["dcTMD friction correction"]@{ shape: process }
+34 --> 35
+```
+
+## Create GRO and TOP complex files
+
+```mermaid
+graph LR
+0["Ligand SDF"]@{ shape: doc }
+1["pH"]@{ shape: lean-l }
+2["Apoprotein PDB"]@{ shape: doc }
+3["Water model"]@{ shape: lean-l }
+4["Force field"]@{ shape: lean-l }
+5["Descriptors"]@{ shape: process }
+0 --> 5
+6["Compound conversion"]@{ shape: process }
+0 --> 6
+1 --> 6
+7["GROMACS initial setup"]@{ shape: process }
+4 --> 7
+2 --> 7
+3 --> 7
+8["Cut"]@{ shape: process }
+5 --> 8
+9["Search in textfiles"]@{ shape: process }
+6 --> 9
+10["Parse parameter value"]@{ shape: process }
+8 --> 10
+11["AnteChamber"]@{ shape: process }
+10 --> 11
+9 --> 11
+12["Generate MD topologies for small molecules"]@{ shape: process }
+10 --> 12
+11 --> 12
+13["Merge GROMACS topologies"]@{ shape: process }
+12 --> 13
+12 --> 13
+7 --> 13
+7 --> 13
+```
diff --git a/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa_diagrams.md b/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa_diagrams.md
new file mode 100644
index 000000000..91e6263c1
--- /dev/null
+++ b/workflows/computational-chemistry/gromacs-mmgbsa/gromacs-mmgbsa_diagrams.md
@@ -0,0 +1,113 @@
+# Workflow diagrams
+
+## MMGBSA calculations with GROMACS
+
+```mermaid
+graph LR
+0["Salt concentration"]@{ shape: lean-l }
+1["Number of simulations"]@{ shape: lean-l }
+2["Apoprotein PDB"]@{ shape: doc }
+3["Water model"]@{ shape: lean-l }
+4["pH"]@{ shape: lean-l }
+5["Force field"]@{ shape: lean-l }
+6["Ligand SDF"]@{ shape: doc }
+7["NVT equilibration steps"]@{ shape: lean-l }
+8["NPT equilibration steps"]@{ shape: lean-l }
+9["Production steps"]@{ shape: lean-l }
+10["Compose text parameter value"]@{ shape: process }
+0 --> 10
+11["Create GRO and TOP complex files"]@{ shape: subprocess }
+2 --> 11
+5 --> 11
+6 --> 11
+3 --> 11
+4 --> 11
+12["Create text file"]@{ shape: process }
+10 --> 12
+1 --> 12
+13["GROMACS structure configuration"]@{ shape: process }
+11 --> 13
+14["Split file"]@{ shape: process }
+12 --> 14
+15["Parse parameter value"]@{ shape: process }
+14 --> 15
+16["GROMACS solvation and adding ions"]@{ shape: process }
+15 --> 16
+13 --> 16
+11 --> 16
+17["GROMACS energy minimization"]@{ shape: process }
+16 --> 17
+16 --> 17
+18["Convert Parameters"]@{ shape: process }
+16 --> 18
+16 --> 18
+19["GROMACS simulation"]@{ shape: process }
+17 --> 19
+11 --> 19
+7 --> 19
+16 --> 19
+20["GROMACS simulation"]@{ shape: process }
+19 --> 20
+19 --> 20
+11 --> 20
+8 --> 20
+16 --> 20
+21["GROMACS simulation"]@{ shape: process }
+20 --> 21
+20 --> 21
+9 --> 21
+16 --> 21
+22["MDTraj file converter"]@{ shape: process }
+21 --> 22
+23["MMPBSA/MMGBSA"]@{ shape: process }
+18 --> 23
+18 --> 23
+18 --> 23
+18 --> 23
+22 --> 23
+24["Search in textfiles"]@{ shape: process }
+23 --> 24
+25["Collapse Collection"]@{ shape: process }
+24 --> 25
+26["Cut"]@{ shape: process }
+25 --> 26
+27["Summary Statistics"]@{ shape: process }
+26 --> 27
+```
+
+## Create GRO and TOP complex files
+
+```mermaid
+graph LR
+0["Ligand SDF"]@{ shape: doc }
+1["pH"]@{ shape: lean-l }
+2["Apoprotein PDB"]@{ shape: doc }
+3["Water model"]@{ shape: lean-l }
+4["Force field"]@{ shape: lean-l }
+5["Descriptors"]@{ shape: process }
+0 --> 5
+6["Compound conversion"]@{ shape: process }
+0 --> 6
+1 --> 6
+7["GROMACS initial setup"]@{ shape: process }
+4 --> 7
+2 --> 7
+3 --> 7
+8["Cut"]@{ shape: process }
+5 --> 8
+9["Search in textfiles"]@{ shape: process }
+6 --> 9
+10["Parse parameter value"]@{ shape: process }
+8 --> 10
+11["AnteChamber"]@{ shape: process }
+10 --> 11
+9 --> 11
+12["Generate MD topologies for small molecules"]@{ shape: process }
+10 --> 12
+11 --> 12
+13["Merge GROMACS topologies"]@{ shape: process }
+12 --> 13
+12 --> 13
+7 --> 13
+7 --> 13
+```
diff --git a/workflows/computational-chemistry/protein-ligand-complex-parameterization/protein-ligand-complex-parameterization_diagrams.md b/workflows/computational-chemistry/protein-ligand-complex-parameterization/protein-ligand-complex-parameterization_diagrams.md
new file mode 100644
index 000000000..e47331f22
--- /dev/null
+++ b/workflows/computational-chemistry/protein-ligand-complex-parameterization/protein-ligand-complex-parameterization_diagrams.md
@@ -0,0 +1,38 @@
+# Workflow diagrams
+
+## Create GRO and TOP complex files
+
+```mermaid
+graph LR
+0["pH"]@{ shape: lean-l }
+1["Ligand SDF"]@{ shape: doc }
+2["Apoprotein PDB"]@{ shape: doc }
+3["Water model"]@{ shape: lean-l }
+4["Force field"]@{ shape: lean-l }
+5["Compound conversion"]@{ shape: process }
+1 --> 5
+0 --> 5
+6["Descriptors"]@{ shape: process }
+1 --> 6
+7["GROMACS initial setup"]@{ shape: process }
+4 --> 7
+2 --> 7
+3 --> 7
+8["Search in textfiles"]@{ shape: process }
+5 --> 8
+9["Cut"]@{ shape: process }
+6 --> 9
+10["Parse parameter value"]@{ shape: process }
+9 --> 10
+11["AnteChamber"]@{ shape: process }
+10 --> 11
+8 --> 11
+12["Generate MD topologies for small molecules"]@{ shape: process }
+10 --> 12
+11 --> 12
+13["Merge GROMACS topologies"]@{ shape: process }
+12 --> 13
+12 --> 13
+7 --> 13
+7 --> 13
+```
diff --git a/workflows/data-fetching/parallel-accession-download/parallel-accession-download_diagrams.md b/workflows/data-fetching/parallel-accession-download/parallel-accession-download_diagrams.md
new file mode 100644
index 000000000..189bf2b8c
--- /dev/null
+++ b/workflows/data-fetching/parallel-accession-download/parallel-accession-download_diagrams.md
@@ -0,0 +1,16 @@
+# Workflow diagrams
+
+## Parallel Accession Download
+
+```mermaid
+graph LR
+0["Run accessions"]@{ shape: doc }
+1["Split accessions to collection"]@{ shape: process }
+0 --> 1
+2["fasterq-dump"]@{ shape: process }
+1 --> 2
+3["flatten paired output"]@{ shape: process }
+2 --> 3
+4["flatten single end output"]@{ shape: process }
+2 --> 4
+```
diff --git a/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs_diagrams.md b/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs_diagrams.md
new file mode 100644
index 000000000..9dcad63ef
--- /dev/null
+++ b/workflows/data-fetching/sra-manifest-to-concatenated-fastqs/sra-manifest-to-concatenated-fastqs_diagrams.md
@@ -0,0 +1,40 @@
+# Workflow diagrams
+
+## sra_manifest_to_concatenated_fastqs_parallel
+
+```mermaid
+graph LR
+0["SRA_manifest"]@{ shape: doc }
+1["Column number with SRA ID"]@{ shape: lean-l }
+2["Column number with final identifier"]@{ shape: lean-l }
+3["Set SRA column to 1 if at 0"]@{ shape: process }
+1 --> 3
+4["Compute column expression"]@{ shape: process }
+3 --> 4
+2 --> 4
+5["Cut columns of interest"]@{ shape: process }
+4 --> 5
+0 --> 5
+6["generate table for relabelling"]@{ shape: process }
+5 --> 6
+7["Cut to get only SRA"]@{ shape: process }
+5 --> 7
+8["split file to get one SRA per file + header"]@{ shape: process }
+7 --> 8
+9["get Fastqs from SRA IDs"]@{ shape: process }
+8 --> 9
+10["relabel pair collec to get SRA+sample"]@{ shape: process }
+6 --> 10
+9 --> 10
+11["relabel single collec to get SRA+sample"]@{ shape: process }
+6 --> 11
+9 --> 11
+12["Apply rules"]@{ shape: process }
+10 --> 12
+13["Apply rules"]@{ shape: process }
+11 --> 13
+14["Concatenate multiple datasets"]@{ shape: process }
+12 --> 14
+15["Concatenate multiple datasets"]@{ shape: process }
+13 --> 15
+```
diff --git a/workflows/epigenetics/atacseq/atacseq_diagrams.md b/workflows/epigenetics/atacseq/atacseq_diagrams.md
new file mode 100644
index 000000000..5e0f45542
--- /dev/null
+++ b/workflows/epigenetics/atacseq/atacseq_diagrams.md
@@ -0,0 +1,80 @@
+# Workflow diagrams
+
+## ATACseq
+
+```mermaid
+graph LR
+0["PE fastq input"]@{ shape: docs }
+1["reference_genome"]@{ shape: lean-l }
+2["effective_genome_size"]@{ shape: lean-l }
+3["bin_size"]@{ shape: lean-l }
+4["Cutadapt (remove adapter + bad quality bases)"]@{ shape: process }
+0 --> 4
+5["Bowtie2 map on reference"]@{ shape: process }
+4 --> 5
+1 --> 5
+6["filter MAPQ30 concordant pairs and not mitochondrial pairs"]@{ shape: process }
+5 --> 6
+7["Get number of reads per chromosome"]@{ shape: process }
+5 --> 7
+8["remove PCR duplicates"]@{ shape: process }
+6 --> 8
+9["reads in chrM/MT for multiQC"]@{ shape: process }
+7 --> 9
+10["convert BAM to BED to improve peak calling"]@{ shape: process }
+8 --> 10
+11["Compute fragment length histogram"]@{ shape: process }
+8 --> 11
+12["number of reads"]@{ shape: process }
+8 --> 12
+13["Call Peak with MACS2"]@{ shape: process }
+2 --> 13
+10 --> 13
+14["remove comments lines"]@{ shape: process }
+11 --> 14
+15["compute 1/million reads"]@{ shape: process }
+12 --> 15
+16["Bigwig from MACS2 (no norm)"]@{ shape: process }
+13 --> 16
+17["get summits +/-500kb"]@{ shape: process }
+1 --> 17
+13 --> 17
+18["summary of MACS2"]@{ shape: process }
+13 --> 18
+19["Convert 1/million reads to parameter"]@{ shape: process }
+15 --> 19
+20["Isolate each bigwig do normalize not average"]@{ shape: process }
+16 --> 20
+21["Merge summits +/-500kb"]@{ shape: process }
+17 --> 21
+22["normalize by million reads"]@{ shape: process }
+3 --> 22
+19 --> 22
+20 --> 22
+23["Compute coverage on summits +/-500kb"]@{ shape: process }
+21 --> 23
+8 --> 23
+24["number of reads in peaks"]@{ shape: process }
+23 --> 24
+25["compute 1/million reads in peaks"]@{ shape: process }
+24 --> 25
+26["Combine number of reads in peaks with total number of reads"]@{ shape: process }
+24 --> 26
+12 --> 26
+27["Convert 1/million reads in peaks to parameter"]@{ shape: process }
+25 --> 27
+28["reads in peaks multiQC"]@{ shape: process }
+26 --> 28
+29["normalize by million reads in peaks"]@{ shape: process }
+3 --> 29
+27 --> 29
+20 --> 29
+30["MultiQC"]@{ shape: process }
+4 --> 30
+5 --> 30
+9 --> 30
+8 --> 30
+14 --> 30
+13 --> 30
+28 --> 30
+```
diff --git a/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates_diagrams.md b/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates_diagrams.md
new file mode 100644
index 000000000..2012fce1d
--- /dev/null
+++ b/workflows/epigenetics/average-bigwig-between-replicates/average-bigwig-between-replicates_diagrams.md
@@ -0,0 +1,14 @@
+# Workflow diagrams
+
+## Average Bigwig between replicates
+
+```mermaid
+graph LR
+0["Bigwig to average"]@{ shape: docs }
+1["bin_size"]@{ shape: lean-l }
+2["Apply rules"]@{ shape: process }
+0 --> 2
+3["average bigwigs from different replicates"]@{ shape: process }
+1 --> 3
+2 --> 3
+```
diff --git a/workflows/epigenetics/chipseq-pe/chipseq-pe_diagrams.md b/workflows/epigenetics/chipseq-pe/chipseq-pe_diagrams.md
new file mode 100644
index 000000000..eb25874fe
--- /dev/null
+++ b/workflows/epigenetics/chipseq-pe/chipseq-pe_diagrams.md
@@ -0,0 +1,34 @@
+# Workflow diagrams
+
+## ChIPseq_PE
+
+```mermaid
+graph LR
+0["PE fastq input"]@{ shape: docs }
+1["adapter_forward"]@{ shape: lean-l }
+2["adapter_reverse"]@{ shape: lean-l }
+3["reference_genome"]@{ shape: lean-l }
+4["effective_genome_size"]@{ shape: lean-l }
+5["normalize_profile"]@{ shape: lean-l }
+6["Cutadapt (remove adapter + bad quality bases)"]@{ shape: process }
+0 --> 6
+1 --> 6
+2 --> 6
+7["Bowtie2 map on reference"]@{ shape: process }
+6 --> 7
+3 --> 7
+8["filter MAPQ30 concordent pairs"]@{ shape: process }
+7 --> 8
+9["Call Peaks with MACS2"]@{ shape: process }
+5 --> 9
+4 --> 9
+8 --> 9
+10["summary of MACS2"]@{ shape: process }
+9 --> 10
+11["Bigwig from MACS2"]@{ shape: process }
+9 --> 11
+12["MultiQC"]@{ shape: process }
+6 --> 12
+7 --> 12
+9 --> 12
+```
diff --git a/workflows/epigenetics/chipseq-sr/chipseq-sr_diagrams.md b/workflows/epigenetics/chipseq-sr/chipseq-sr_diagrams.md
new file mode 100644
index 000000000..cacacd1a3
--- /dev/null
+++ b/workflows/epigenetics/chipseq-sr/chipseq-sr_diagrams.md
@@ -0,0 +1,32 @@
+# Workflow diagrams
+
+## ChIPseq_SR
+
+```mermaid
+graph LR
+0["SR fastq input"]@{ shape: docs }
+1["adapter_forward"]@{ shape: lean-l }
+2["reference_genome"]@{ shape: lean-l }
+3["effective_genome_size"]@{ shape: lean-l }
+4["normalize_profile"]@{ shape: lean-l }
+5["Cutadapt (remove adapter + bad quality bases)"]@{ shape: process }
+0 --> 5
+1 --> 5
+6["Bowtie2 map on reference"]@{ shape: process }
+5 --> 6
+2 --> 6
+7["filter MAPQ30"]@{ shape: process }
+6 --> 7
+8["Call Peaks with MACS2"]@{ shape: process }
+4 --> 8
+3 --> 8
+7 --> 8
+9["summary of MACS2"]@{ shape: process }
+8 --> 9
+10["Bigwig from MACS2"]@{ shape: process }
+8 --> 10
+11["MultiQC"]@{ shape: process }
+5 --> 11
+6 --> 11
+8 --> 11
+```
diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun_diagrams.md b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun_diagrams.md
new file mode 100644
index 000000000..df45458c8
--- /dev/null
+++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-atac-cutandrun_diagrams.md
@@ -0,0 +1,67 @@
+# Workflow diagrams
+
+## Get Confident Peaks From ATAC or CUTandRUN replicates
+
+```mermaid
+graph LR
+0["n rmDup BAM"]@{ shape: docs }
+1["Minimum number of overlap"]@{ shape: lean-l }
+2["effective_genome_size"]@{ shape: lean-l }
+3["bin_size"]@{ shape: lean-l }
+4["convert BAM to BED"]@{ shape: process }
+0 --> 4
+5["count number of reads"]@{ shape: process }
+0 --> 5
+6["generate filter rule"]@{ shape: process }
+1 --> 6
+7["call peaks individually"]@{ shape: process }
+2 --> 7
+4 --> 7
+8["put all nb of reads into single dataset"]@{ shape: process }
+5 --> 8
+9["compute multi intersect"]@{ shape: process }
+7 --> 9
+10["individual normalized bigwig"]@{ shape: process }
+7 --> 10
+11["get min value"]@{ shape: process }
+8 --> 11
+12["get nb of replicates"]@{ shape: process }
+8 --> 12
+13["filter multi intersect"]@{ shape: process }
+6 --> 13
+9 --> 13
+14["average coverage from replicates"]@{ shape: process }
+3 --> 14
+10 --> 14
+15["convert min value to text"]@{ shape: process }
+11 --> 15
+16["Parse parameter value"]@{ shape: process }
+12 --> 16
+17["create a dataset with the min value as many times as there are replicates"]@{ shape: process }
+15 --> 17
+16 --> 17
+18["split min value"]@{ shape: process }
+17 --> 18
+19["convert min nb of reads to parameter"]@{ shape: process }
+18 --> 19
+20["select random reads"]@{ shape: process }
+0 --> 20
+19 --> 20
+21["convert subsampled bam to bed"]@{ shape: process }
+20 --> 21
+22["call peaks on merge"]@{ shape: process }
+2 --> 22
+21 --> 22
+23["get merged peaks overlapping at least x replicates"]@{ shape: process }
+22 --> 23
+13 --> 23
+24["multiQC"]@{ shape: process }
+7 --> 24
+22 --> 24
+25["only keep peaks with summits overlapping intersection of at least x replicates"]@{ shape: process }
+23 --> 25
+26["keep only columns of narrowPeak"]@{ shape: process }
+25 --> 26
+27["discard duplicated lines"]@{ shape: process }
+26 --> 27
+```
diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe_diagrams.md b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe_diagrams.md
new file mode 100644
index 000000000..de9160e21
--- /dev/null
+++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-pe_diagrams.md
@@ -0,0 +1,63 @@
+# Workflow diagrams
+
+## Get Confident Peaks From ChIP_PE replicates
+
+```mermaid
+graph LR
+0["n rmDup BAMPE"]@{ shape: docs }
+1["Minimum number of overlap"]@{ shape: lean-l }
+2["effective_genome_size"]@{ shape: lean-l }
+3["bin_size"]@{ shape: lean-l }
+4["count number of reads"]@{ shape: process }
+0 --> 4
+5["generate filter rule"]@{ shape: process }
+1 --> 5
+6["call peaks individually"]@{ shape: process }
+2 --> 6
+0 --> 6
+7["put all nb of reads into single dataset"]@{ shape: process }
+4 --> 7
+8["compute multi intersect"]@{ shape: process }
+6 --> 8
+9["individual normalized bigwig"]@{ shape: process }
+6 --> 9
+10["get min value"]@{ shape: process }
+7 --> 10
+11["get nb of replicates"]@{ shape: process }
+7 --> 11
+12["filter multi intersect"]@{ shape: process }
+5 --> 12
+8 --> 12
+13["average coverage from replicates"]@{ shape: process }
+3 --> 13
+9 --> 13
+14["convert min value to text"]@{ shape: process }
+10 --> 14
+15["Parse parameter value"]@{ shape: process }
+11 --> 15
+16["create a dataset with the min value as many times as there are replicates"]@{ shape: process }
+14 --> 16
+15 --> 16
+17["split min value"]@{ shape: process }
+16 --> 17
+18["convert min nb of reads to parameter"]@{ shape: process }
+17 --> 18
+19["downsample BAM"]@{ shape: process }
+0 --> 19
+18 --> 19
+20["call peaks on merge"]@{ shape: process }
+2 --> 20
+19 --> 20
+21["get merged peaks overlapping at least x replicates"]@{ shape: process }
+20 --> 21
+12 --> 21
+22["multiQC"]@{ shape: process }
+6 --> 22
+20 --> 22
+23["only keep peaks with summits overlapping intersection of at least x replicates"]@{ shape: process }
+21 --> 23
+24["keep only columns of narrowPeak"]@{ shape: process }
+23 --> 24
+25["discard duplicated lines"]@{ shape: process }
+24 --> 25
+```
diff --git a/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr_diagrams.md b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr_diagrams.md
new file mode 100644
index 000000000..52faf7045
--- /dev/null
+++ b/workflows/epigenetics/consensus-peaks/consensus-peaks-chip-sr_diagrams.md
@@ -0,0 +1,63 @@
+# Workflow diagrams
+
+## Get Confident Peaks From ChIP_SR replicates
+
+```mermaid
+graph LR
+0["n rmDup BAMSR"]@{ shape: docs }
+1["Minimum number of overlap"]@{ shape: lean-l }
+2["effective_genome_size"]@{ shape: lean-l }
+3["bin_size"]@{ shape: lean-l }
+4["count number of reads"]@{ shape: process }
+0 --> 4
+5["generate filter rule"]@{ shape: process }
+1 --> 5
+6["call peaks individually"]@{ shape: process }
+2 --> 6
+0 --> 6
+7["put all nb of reads into single dataset"]@{ shape: process }
+4 --> 7
+8["compute multi intersect"]@{ shape: process }
+6 --> 8
+9["individual normalized bigwig"]@{ shape: process }
+6 --> 9
+10["get min value"]@{ shape: process }
+7 --> 10
+11["get nb of replicates"]@{ shape: process }
+7 --> 11
+12["filter multi intersect"]@{ shape: process }
+5 --> 12
+8 --> 12
+13["average coverage from replicates"]@{ shape: process }
+3 --> 13
+9 --> 13
+14["convert min value to text"]@{ shape: process }
+10 --> 14
+15["Parse parameter value"]@{ shape: process }
+11 --> 15
+16["create a dataset with the min value as many times as there are replicates"]@{ shape: process }
+14 --> 16
+15 --> 16
+17["split min value"]@{ shape: process }
+16 --> 17
+18["convert min nb of reads to parameter"]@{ shape: process }
+17 --> 18
+19["downsample BAM"]@{ shape: process }
+0 --> 19
+18 --> 19
+20["call peaks on merge"]@{ shape: process }
+2 --> 20
+19 --> 20
+21["get merged peaks overlapping at least x replicates"]@{ shape: process }
+20 --> 21
+12 --> 21
+22["multiQC"]@{ shape: process }
+6 --> 22
+20 --> 22
+23["only keep peaks with summits overlapping intersection of at least x replicates"]@{ shape: process }
+21 --> 23
+24["keep only columns of narrowPeak"]@{ shape: process }
+23 --> 24
+25["discard duplicated lines"]@{ shape: process }
+24 --> 25
+```
diff --git a/workflows/epigenetics/cutandrun/cutandrun_diagrams.md b/workflows/epigenetics/cutandrun/cutandrun_diagrams.md
new file mode 100644
index 000000000..69027007c
--- /dev/null
+++ b/workflows/epigenetics/cutandrun/cutandrun_diagrams.md
@@ -0,0 +1,39 @@
+# Workflow diagrams
+
+## CUTandRUN
+
+```mermaid
+graph LR
+0["PE fastq input"]@{ shape: docs }
+1["adapter_forward"]@{ shape: lean-l }
+2["adapter_reverse"]@{ shape: lean-l }
+3["reference_genome"]@{ shape: lean-l }
+4["effective_genome_size"]@{ shape: lean-l }
+5["normalize_profile"]@{ shape: lean-l }
+6["Cutadapt (remove adapter + bad quality bases)"]@{ shape: process }
+0 --> 6
+1 --> 6
+2 --> 6
+7["Bowtie2 map on reference"]@{ shape: process }
+6 --> 7
+3 --> 7
+8["filter MAPQ30 concordant pairs"]@{ shape: process }
+7 --> 8
+9["remove PCR duplicates"]@{ shape: process }
+8 --> 9
+10["convert BAM to BED to improve peak calling"]@{ shape: process }
+9 --> 10
+11["Call Peaks with MACS2"]@{ shape: process }
+5 --> 11
+4 --> 11
+10 --> 11
+12["summary of MACS2"]@{ shape: process }
+11 --> 12
+13["Bigwig from MACS2"]@{ shape: process }
+11 --> 13
+14["MultiQC"]@{ shape: process }
+6 --> 14
+7 --> 14
+9 --> 14
+11 --> 14
+```
diff --git a/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler_diagrams.md b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler_diagrams.md
new file mode 100644
index 000000000..2b9564a6d
--- /dev/null
+++ b/workflows/epigenetics/hic-hicup-cooler/chic-fastq-to-cool-hicup-cooler_diagrams.md
@@ -0,0 +1,94 @@
+# Workflow diagrams
+
+## cHi-C_fastqToCool_hicup_cooler
+
+```mermaid
+graph LR
+0["PE fastq input"]@{ shape: docs }
+1["genome name"]@{ shape: lean-l }
+2["Restriction enzyme"]@{ shape: lean-l }
+3["No fill-in"]@{ shape: lean-l }
+4["minimum MAPQ"]@{ shape: lean-l }
+5["Bin size in bp"]@{ shape: lean-l }
+6["Interactions to consider to calculate weights in normalization step"]@{ shape: lean-l }
+7["capture region (chromosome)"]@{ shape: lean-l }
+8["capture region (start)"]@{ shape: lean-l }
+9["capture region (end)"]@{ shape: lean-l }
+10["Hi-C_fastqToPairs_hicup"]@{ shape: subprocess }
+3 --> 10
+0 --> 10
+2 --> 10
+1 --> 10
+4 --> 10
+11["write filtering for capture region"]@{ shape: process }
+8 --> 11
+7 --> 11
+9 --> 11
+8 --> 11
+7 --> 11
+9 --> 11
+12["write region for pyGenomeTracks"]@{ shape: process }
+7 --> 12
+8 --> 12
+9 --> 12
+13["Filter for capture region"]@{ shape: process }
+11 --> 13
+10 --> 13
+14["Sort filtered pairs and index"]@{ shape: process }
+13 --> 14
+1 --> 14
+15["Hi-C_juicermediumtabixToCool_cooler"]@{ shape: subprocess }
+5 --> 15
+6 --> 15
+14 --> 15
+1 --> 15
+16["final_plot"]@{ shape: process }
+12 --> 16
+15 --> 16
+```
+
+## Hi-C_juicermediumtabixToCool_cooler
+
+```mermaid
+graph LR
+0["Bin size in bp"]@{ shape: lean-l }
+1["genome name"]@{ shape: lean-l }
+2["Juicer Medium Tabix with validPairs"]@{ shape: docs }
+3["Interactions to consider to calculate weights in normalization step"]@{ shape: lean-l }
+4["make bed with bins"]@{ shape: process }
+0 --> 4
+1 --> 4
+5["Load pairs in matrix"]@{ shape: process }
+1 --> 5
+2 --> 5
+4 --> 5
+6["ICE normalization"]@{ shape: process }
+3 --> 6
+5 --> 6
+```
+
+## Hi-C_fastqToPairs_hicup
+
+```mermaid
+graph LR
+0["PE fastq input"]@{ shape: docs }
+1["genome name"]@{ shape: lean-l }
+2["Restriction enzyme"]@{ shape: lean-l }
+3["No fill-in"]@{ shape: lean-l }
+4["minimum MAPQ"]@{ shape: lean-l }
+5["HiCUP"]@{ shape: process }
+3 --> 5
+1 --> 5
+0 --> 5
+2 --> 5
+1 --> 5
+6["build filtering rule for MAPQ"]@{ shape: process }
+4 --> 6
+4 --> 6
+7["valid pairs in juicebox format"]@{ shape: process }
+5 --> 7
+5 --> 7
+8["valid pairs in juicebox format MAPQ filtered"]@{ shape: process }
+6 --> 8
+7 --> 8
+```
diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler_diagrams.md b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler_diagrams.md
new file mode 100644
index 000000000..43f82f701
--- /dev/null
+++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-cool-hicup-cooler_diagrams.md
@@ -0,0 +1,78 @@
+# Workflow diagrams
+
+## Hi-C_fastqToCool_hicup_cooler
+
+```mermaid
+graph LR
+0["PE fastq input"]@{ shape: docs }
+1["genome name"]@{ shape: lean-l }
+2["Restriction enzyme"]@{ shape: lean-l }
+3["No fill-in"]@{ shape: lean-l }
+4["minimum MAPQ"]@{ shape: lean-l }
+5["Bin size in bp"]@{ shape: lean-l }
+6["Interactions to consider to calculate weights in normalization step"]@{ shape: lean-l }
+7["region for matrix plotting"]@{ shape: lean-l }
+8["Hi-C_fastqToPairs_hicup"]@{ shape: subprocess }
+3 --> 8
+0 --> 8
+2 --> 8
+1 --> 8
+4 --> 8
+9["Sort pairs and index"]@{ shape: process }
+8 --> 9
+1 --> 9
+10["Hi-C_juicermediumtabixToCool_cooler"]@{ shape: subprocess }
+5 --> 10
+6 --> 10
+9 --> 10
+1 --> 10
+11["final plot"]@{ shape: process }
+7 --> 11
+10 --> 11
+```
+
+## Hi-C_juicermediumtabixToCool_cooler
+
+```mermaid
+graph LR
+0["Bin size in bp"]@{ shape: lean-l }
+1["genome name"]@{ shape: lean-l }
+2["Juicer Medium Tabix with validPairs"]@{ shape: docs }
+3["Interactions to consider to calculate weights in normalization step"]@{ shape: lean-l }
+4["make bed with bins"]@{ shape: process }
+0 --> 4
+1 --> 4
+5["Load pairs in matrix"]@{ shape: process }
+1 --> 5
+2 --> 5
+4 --> 5
+6["ICE normalization"]@{ shape: process }
+3 --> 6
+5 --> 6
+```
+
+## Hi-C_fastqToPairs_hicup
+
+```mermaid
+graph LR
+0["PE fastq input"]@{ shape: docs }
+1["genome name"]@{ shape: lean-l }
+2["Restriction enzyme"]@{ shape: lean-l }
+3["No fill-in"]@{ shape: lean-l }
+4["minimum MAPQ"]@{ shape: lean-l }
+5["HiCUP"]@{ shape: process }
+3 --> 5
+1 --> 5
+0 --> 5
+2 --> 5
+1 --> 5
+6["build filtering rule for MAPQ"]@{ shape: process }
+4 --> 6
+4 --> 6
+7["valid pairs in juicebox format"]@{ shape: process }
+5 --> 7
+5 --> 7
+8["valid pairs in juicebox format MAPQ filtered"]@{ shape: process }
+6 --> 8
+7 --> 8
+```
diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup_diagrams.md b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup_diagrams.md
new file mode 100644
index 000000000..087439ce1
--- /dev/null
+++ b/workflows/epigenetics/hic-hicup-cooler/hic-fastq-to-pairs-hicup_diagrams.md
@@ -0,0 +1,27 @@
+# Workflow diagrams
+
+## Hi-C_fastqToPairs_hicup
+
+```mermaid
+graph LR
+0["PE fastq input"]@{ shape: docs }
+1["genome name"]@{ shape: lean-l }
+2["Restriction enzyme"]@{ shape: lean-l }
+3["No fill-in"]@{ shape: lean-l }
+4["minimum MAPQ"]@{ shape: lean-l }
+5["HiCUP"]@{ shape: process }
+3 --> 5
+1 --> 5
+0 --> 5
+2 --> 5
+1 --> 5
+6["build filtering rule for MAPQ"]@{ shape: process }
+4 --> 6
+4 --> 6
+7["valid pairs in juicebox format"]@{ shape: process }
+5 --> 7
+5 --> 7
+8["valid pairs in juicebox format MAPQ filtered"]@{ shape: process }
+6 --> 8
+7 --> 8
+```
diff --git a/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler_diagrams.md b/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler_diagrams.md
new file mode 100644
index 000000000..ff1461972
--- /dev/null
+++ b/workflows/epigenetics/hic-hicup-cooler/hic-juicermediumtabix-to-cool-cooler_diagrams.md
@@ -0,0 +1,21 @@
+# Workflow diagrams
+
+## Hi-C_juicermediumtabixToCool_cooler
+
+```mermaid
+graph LR
+0["Bin size in bp"]@{ shape: lean-l }
+1["genome name"]@{ shape: lean-l }
+2["Juicer Medium Tabix with validPairs"]@{ shape: docs }
+3["Interactions to consider to calculate weights in normalization step"]@{ shape: lean-l }
+4["make bed with bins"]@{ shape: process }
+0 --> 4
+1 --> 4
+5["Load pairs in matrix"]@{ shape: process }
+1 --> 5
+2 --> 5
+4 --> 5
+6["ICE normalization"]@{ shape: process }
+3 --> 6
+5 --> 6
+```
diff --git a/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye_diagrams.md b/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye_diagrams.md
new file mode 100644
index 000000000..89f618224
--- /dev/null
+++ b/workflows/genome-assembly/assembly-with-flye/Genome-assembly-with-Flye_diagrams.md
@@ -0,0 +1,16 @@
+# Workflow diagrams
+
+## Genome assembly with Flye
+
+```mermaid
+graph LR
+0["Input sequence reads"]@{ shape: doc }
+1["Flye: assembly"]@{ shape: process }
+0 --> 1
+2["Quast genome report"]@{ shape: process }
+1 --> 2
+3["Fasta statistics"]@{ shape: process }
+1 --> 3
+4["Bandage image: Flye assembly"]@{ shape: process }
+1 --> 4
+```
diff --git a/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly_diagrams.md b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly_diagrams.md
new file mode 100644
index 000000000..fb737d0bd
--- /dev/null
+++ b/workflows/genome-assembly/bacterial-genome-assembly/bacterial_genome_assembly_diagrams.md
@@ -0,0 +1,33 @@
+# Workflow diagrams
+
+## Bacterial Genome Assembly using Shovill
+
+```mermaid
+graph LR
+0["Input adapter trimmed sequence reads (forward)"]@{ shape: doc }
+1["Input adapter trimmed sequence reads (reverse)"]@{ shape: doc }
+2["shovill_genome_assembly"]@{ shape: process }
+0 --> 2
+1 --> 2
+3["quast_quality"]@{ shape: process }
+2 --> 3
+0 --> 3
+1 --> 3
+4["refseqmasher_genome"]@{ shape: process }
+2 --> 4
+5["bandage_contig_graph_stats"]@{ shape: process }
+2 --> 5
+6["bandage_contig_graph_plot"]@{ shape: process }
+2 --> 6
+7["ToolDistillator"]@{ shape: process }
+2 --> 7
+2 --> 7
+2 --> 7
+3 --> 7
+3 --> 7
+4 --> 7
+6 --> 7
+5 --> 7
+8["ToolDistillator summarize"]@{ shape: process }
+7 --> 8
+```
diff --git a/workflows/genome-assembly/polish-with-long-reads/Assembly-polishing-with-long-reads_diagrams.md b/workflows/genome-assembly/polish-with-long-reads/Assembly-polishing-with-long-reads_diagrams.md
new file mode 100644
index 000000000..45a415547
--- /dev/null
+++ b/workflows/genome-assembly/polish-with-long-reads/Assembly-polishing-with-long-reads_diagrams.md
@@ -0,0 +1,42 @@
+# Workflow diagrams
+
+## Assembly polishing with long reads
+
+```mermaid
+graph LR
+0["Assembly to be polished"]@{ shape: doc }
+1["long reads"]@{ shape: doc }
+2["minimap setting (for long reads) "]@{ shape: lean-l }
+3["Minimap2: map long reads to assembly"]@{ shape: process }
+2 --> 3
+1 --> 3
+0 --> 3
+4["Racon: polish 1"]@{ shape: process }
+0 --> 4
+3 --> 4
+1 --> 4
+5["Minimap2: map long reads to polished assembly 1"]@{ shape: process }
+2 --> 5
+1 --> 5
+4 --> 5
+6["Racon: polish 2"]@{ shape: process }
+4 --> 6
+5 --> 6
+1 --> 6
+7["Minimap2: map long reads to polished assembly 2"]@{ shape: process }
+2 --> 7
+1 --> 7
+6 --> 7
+8["Racon: polish 3"]@{ shape: process }
+6 --> 8
+7 --> 8
+1 --> 8
+9["Minimap2: map long reads to polished assembly 3"]@{ shape: process }
+2 --> 9
+1 --> 9
+8 --> 9
+10["Racon: polish 4"]@{ shape: process }
+8 --> 10
+9 --> 10
+1 --> 10
+```
diff --git a/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control_diagrams.md b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control_diagrams.md
new file mode 100644
index 000000000..94170e132
--- /dev/null
+++ b/workflows/genome-assembly/quality-and-contamination-control/quality_and_contamination_control_diagrams.md
@@ -0,0 +1,41 @@
+# Workflow diagrams
+
+## Quality and Contamination Control For Genome Assembly
+
+```mermaid
+graph LR
+0["Input sequence reads (forward)"]@{ shape: doc }
+1["Input sequence reads (reverse)"]@{ shape: doc }
+2["Select a taxonomy database"]@{ shape: lean-l }
+3["Select a NCBI taxonomy database"]@{ shape: lean-l }
+4["fastp_trimming_step"]@{ shape: process }
+0 --> 4
+1 --> 4
+5["kraken_taxonomy_assignation"]@{ shape: process }
+2 --> 5
+4 --> 5
+4 --> 5
+6["bracken_abundance_estimation"]@{ shape: process }
+5 --> 6
+2 --> 6
+7["recentrifuge_taxonomy_visualization"]@{ shape: process }
+3 --> 7
+5 --> 7
+8["ToolDistillator"]@{ shape: process }
+4 --> 8
+4 --> 8
+4 --> 8
+4 --> 8
+5 --> 8
+2 --> 8
+5 --> 8
+6 --> 8
+6 --> 8
+2 --> 8
+7 --> 8
+7 --> 8
+7 --> 8
+3 --> 8
+9["ToolDistillator summarize"]@{ shape: process }
+8 --> 9
+```
diff --git a/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting_diagrams.md b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting_diagrams.md
new file mode 100644
index 000000000..2308620cd
--- /dev/null
+++ b/workflows/imaging/fluorescence-nuclei-segmentation-and-counting/segmentation-and-counting_diagrams.md
@@ -0,0 +1,23 @@
+# Workflow diagrams
+
+## Segmentation and counting of cell nuclei in fluorescence microscopy images
+
+```mermaid
+graph LR
+0["input_image"]@{ shape: doc }
+1["Filter 2-D image"]@{ shape: process }
+0 --> 1
+2["Perform histogram equalization"]@{ shape: process }
+0 --> 2
+3["Threshold image"]@{ shape: process }
+1 --> 3
+4["Convert image format"]@{ shape: process }
+2 --> 4
+5["Convert binary image to label map"]@{ shape: process }
+3 --> 5
+6["Overlay images"]@{ shape: process }
+4 --> 6
+5 --> 6
+7["Count objects in label map"]@{ shape: process }
+5 --> 7
+```
diff --git a/workflows/metabomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS_diagrams.md b/workflows/metabomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS_diagrams.md
new file mode 100644
index 000000000..b6d81c7f4
--- /dev/null
+++ b/workflows/metabomics/gcms-metams/Mass-spectrometry__GCMS-with-metaMS_diagrams.md
@@ -0,0 +1,29 @@
+# Workflow diagrams
+
+## Mass spectrometry: GCMS with metaMS
+
+```mermaid
+graph LR
+0["Mass-spectrometry Dataset Collection"]@{ shape: docs }
+1["sampleMetadata"]@{ shape: doc }
+2["MSnbase readMSData"]@{ shape: process }
+0 --> 2
+3["xcms findChromPeaks (xcmsSet)"]@{ shape: process }
+2 --> 3
+4["xcms plot chromatogram"]@{ shape: process }
+3 --> 4
+1 --> 4
+5["xcms findChromPeaks Merger"]@{ shape: process }
+3 --> 5
+1 --> 5
+6["metaMS.runGC"]@{ shape: process }
+5 --> 6
+7["Check Format"]@{ shape: process }
+6 --> 7
+1 --> 7
+6 --> 7
+8["Multivariate"]@{ shape: process }
+7 --> 8
+7 --> 8
+7 --> 8
+```
diff --git a/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS_diagrams.md b/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS_diagrams.md
new file mode 100644
index 000000000..dd59f41f7
--- /dev/null
+++ b/workflows/metabomics/lcms-preprocessing/Mass_spectrometry__LC-MS_preprocessing_with_XCMS_diagrams.md
@@ -0,0 +1,36 @@
+# Workflow diagrams
+
+## Mass spectrometry: LC-MS preprocessing with XCMS
+
+```mermaid
+graph LR
+0["SampleMetadata"]@{ shape: doc }
+1["Mass-spectrometry Dataset Collection"]@{ shape: docs }
+2["MSnbase readMSData"]@{ shape: process }
+1 --> 2
+3["xcms plot chromatogram"]@{ shape: process }
+2 --> 3
+0 --> 3
+4["xcms findChromPeaks (xcmsSet)"]@{ shape: process }
+2 --> 4
+5["xcms findChromPeaks Merger"]@{ shape: process }
+4 --> 5
+0 --> 5
+6["xcms groupChromPeaks (group)"]@{ shape: process }
+5 --> 6
+7["xcms adjustRtime (retcor)"]@{ shape: process }
+6 --> 7
+8["Intensity Check"]@{ shape: process }
+6 --> 8
+0 --> 8
+6 --> 8
+9["xcms plot chromatogram"]@{ shape: process }
+7 --> 9
+0 --> 9
+10["xcms groupChromPeaks (group)"]@{ shape: process }
+7 --> 10
+11["xcms fillChromPeaks (fillPeaks)"]@{ shape: process }
+10 --> 11
+12["CAMERA.annotate"]@{ shape: process }
+11 --> 12
+```
diff --git a/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification_diagrams.md b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification_diagrams.md
new file mode 100644
index 000000000..700498dd3
--- /dev/null
+++ b/workflows/microbiome/allele-based-pathogen-identification/Allele-based-Pathogen-Identification_diagrams.md
@@ -0,0 +1,62 @@
+# Workflow diagrams
+
+## Allele-based Pathogen Identification
+
+```mermaid
+graph LR
+0["collection_of_preprocessed_samples"]@{ shape: docs }
+1["samples_profile"]@{ shape: lean-l }
+2["reference_genome_of_tested_strain"]@{ shape: doc }
+3["Convert compressed file to uncompressed."]@{ shape: process }
+2 --> 3
+4["Map with minimap2"]@{ shape: process }
+1 --> 4
+0 --> 4
+3 --> 4
+5["Clair3"]@{ shape: process }
+4 --> 5
+3 --> 5
+6["Samtools depth"]@{ shape: process }
+4 --> 6
+7["Samtools coverage"]@{ shape: process }
+4 --> 7
+8["bcftools norm"]@{ shape: process }
+5 --> 8
+3 --> 8
+9["Advanced Cut"]@{ shape: process }
+6 --> 9
+10["Remove beginning"]@{ shape: process }
+7 --> 10
+11["SnpSift Filter"]@{ shape: process }
+8 --> 11
+12["Table Compute"]@{ shape: process }
+9 --> 12
+13["Cut"]@{ shape: process }
+10 --> 13
+14["SnpSift Extract Fields"]@{ shape: process }
+11 --> 14
+15["bcftools consensus"]@{ shape: process }
+11 --> 15
+3 --> 15
+16["Select first"]@{ shape: process }
+13 --> 16
+17["Remove beginning"]@{ shape: process }
+14 --> 17
+18["Collapse Collection"]@{ shape: process }
+16 --> 18
+19["Count"]@{ shape: process }
+17 --> 19
+20["Advanced Cut"]@{ shape: process }
+18 --> 20
+21["Cut"]@{ shape: process }
+19 --> 21
+22["Paste"]@{ shape: process }
+20 --> 22
+12 --> 22
+23["Select first"]@{ shape: process }
+21 --> 23
+24["Collapse Collection"]@{ shape: process }
+23 --> 24
+25["Column Regex Find And Replace"]@{ shape: process }
+24 --> 25
+```
diff --git a/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification_diagrams.md b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification_diagrams.md
new file mode 100644
index 000000000..09bc23794
--- /dev/null
+++ b/workflows/microbiome/gene-based-pathogen-identification/Gene-based-Pathogen-Identification_diagrams.md
@@ -0,0 +1,42 @@
+# Workflow diagrams
+
+## Gene-based Pathogen Identification
+
+```mermaid
+graph LR
+0["collection_of_preprocessed_samples"]@{ shape: docs }
+1["Extract element identifiers"]@{ shape: process }
+0 --> 1
+2["Build list"]@{ shape: process }
+0 --> 2
+3["Split file"]@{ shape: process }
+1 --> 3
+4["Flye"]@{ shape: process }
+2 --> 4
+5["Parse parameter value"]@{ shape: process }
+3 --> 5
+6["medaka consensus pipeline"]@{ shape: process }
+4 --> 6
+0 --> 6
+7["Bandage Image"]@{ shape: process }
+4 --> 7
+8["Compose text parameter value"]@{ shape: process }
+5 --> 8
+9["FASTA-to-Tabular"]@{ shape: process }
+6 --> 9
+10["ABRicate"]@{ shape: process }
+6 --> 10
+11["ABRicate"]@{ shape: process }
+6 --> 11
+12["Replace"]@{ shape: process }
+8 --> 12
+9 --> 12
+13["Replace"]@{ shape: process }
+8 --> 13
+10 --> 13
+14["Replace"]@{ shape: process }
+8 --> 14
+11 --> 14
+15["Tabular-to-FASTA"]@{ shape: process }
+12 --> 15
+```
diff --git a/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing_diagrams.md b/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing_diagrams.md
new file mode 100644
index 000000000..d2186f2ba
--- /dev/null
+++ b/workflows/microbiome/nanopore-pre-processing/Nanopore-Pre-Processing_diagrams.md
@@ -0,0 +1,64 @@
+# Workflow diagrams
+
+## Nanopore Preprocessing
+
+```mermaid
+graph LR
+0["samples_profile"]@{ shape: lean-l }
+1["host_reference_genome"]@{ shape: lean-l }
+2["collection_of_all_samples"]@{ shape: docs }
+3["Porechop"]@{ shape: process }
+2 --> 3
+4["NanoPlot"]@{ shape: process }
+2 --> 4
+5["FastQC"]@{ shape: process }
+2 --> 5
+6["fastp"]@{ shape: process }
+3 --> 6
+7["MultiQC"]@{ shape: process }
+5 --> 7
+8["Map with minimap2"]@{ shape: process }
+0 --> 8
+6 --> 8
+1 --> 8
+9["NanoPlot"]@{ shape: process }
+6 --> 9
+10["FastQC"]@{ shape: process }
+6 --> 10
+11["Split BAM by reads mapping status"]@{ shape: process }
+8 --> 11
+12["Select"]@{ shape: process }
+10 --> 12
+13["Samtools fastx"]@{ shape: process }
+11 --> 13
+14["Samtools fastx"]@{ shape: process }
+11 --> 14
+15["Collapse Collection"]@{ shape: process }
+12 --> 15
+16["Filter failed datasets"]@{ shape: process }
+13 --> 16
+17["Kraken2"]@{ shape: process }
+14 --> 17
+18["Cut"]@{ shape: process }
+15 --> 18
+19["FastQC"]@{ shape: process }
+16 --> 19
+20["Krakentools: Extract Kraken Reads By ID"]@{ shape: process }
+6 --> 20
+17 --> 20
+17 --> 20
+21["Select"]@{ shape: process }
+19 --> 21
+22["Collapse Collection"]@{ shape: process }
+21 --> 22
+23["Cut"]@{ shape: process }
+22 --> 23
+24["Column join"]@{ shape: process }
+25["Compute"]@{ shape: process }
+24 --> 25
+26["Column Regex Find And Replace"]@{ shape: process }
+25 --> 26
+27["MultiQC"]@{ shape: process }
+10 --> 27
+26 --> 27
+```
diff --git a/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation_diagrams.md b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation_diagrams.md
new file mode 100644
index 000000000..aba9381c8
--- /dev/null
+++ b/workflows/microbiome/pathogen-detection-pathogfair-samples-aggregation-and-visualisation/Pathogen-Detection-PathoGFAIR-Samples-Aggregation-and-Visualisation_diagrams.md
@@ -0,0 +1,141 @@
+# Workflow diagrams
+
+## Pathogen Detection PathoGFAIR Samples Aggregation and Visualisation
+
+```mermaid
+graph LR
+0["amr_identified_by_ncbi"]@{ shape: docs }
+1["vfs_of_genes_identified_by_vfdb"]@{ shape: docs }
+2["amrs"]@{ shape: docs }
+3["contigs"]@{ shape: docs }
+4["vfs"]@{ shape: docs }
+5["removed_hosts_percentage_tabular"]@{ shape: doc }
+6["mapping_mean_depth_per_sample"]@{ shape: doc }
+7["mapping_coverage_percentage_per_sample"]@{ shape: doc }
+8["number_of_variants_per_sample"]@{ shape: doc }
+9["metadata"]@{ shape: doc }
+10["Filter failed datasets"]@{ shape: process }
+0 --> 10
+11["Filter failed datasets"]@{ shape: process }
+1 --> 11
+12["Filter failed datasets"]@{ shape: process }
+2 --> 12
+13["Filter failed datasets"]@{ shape: process }
+3 --> 13
+14["Filter failed datasets"]@{ shape: process }
+4 --> 14
+15["Remove beginning"]@{ shape: process }
+10 --> 15
+16["Remove beginning"]@{ shape: process }
+11 --> 16
+17["Remove beginning"]@{ shape: process }
+12 --> 17
+18["Collapse Collection"]@{ shape: process }
+13 --> 18
+19["Collapse Collection"]@{ shape: process }
+14 --> 19
+20["Remove beginning"]@{ shape: process }
+14 --> 20
+21["Count"]@{ shape: process }
+15 --> 21
+22["Count"]@{ shape: process }
+16 --> 22
+23["Group"]@{ shape: process }
+16 --> 23
+24["Unique"]@{ shape: process }
+17 --> 24
+25["Split by group"]@{ shape: process }
+19 --> 25
+26["Unique"]@{ shape: process }
+20 --> 26
+27["Cut"]@{ shape: process }
+21 --> 27
+28["Cut"]@{ shape: process }
+22 --> 28
+29["Filter empty datasets"]@{ shape: process }
+23 --> 29
+30["Cut"]@{ shape: process }
+24 --> 30
+31["Cut"]@{ shape: process }
+25 --> 31
+32["Cut"]@{ shape: process }
+26 --> 32
+33["Collapse Collection"]@{ shape: process }
+27 --> 33
+34["Collapse Collection"]@{ shape: process }
+28 --> 34
+35["Column join"]@{ shape: process }
+29 --> 35
+36["bedtools getfasta"]@{ shape: process }
+18 --> 36
+30 --> 36
+37["Remove beginning"]@{ shape: process }
+31 --> 37
+38["bedtools getfasta"]@{ shape: process }
+18 --> 38
+32 --> 38
+39["Column Regex Find And Replace"]@{ shape: process }
+33 --> 39
+40["Column Regex Find And Replace"]@{ shape: process }
+34 --> 40
+41["Column Regex Find And Replace"]@{ shape: process }
+35 --> 41
+42["Regex Find And Replace"]@{ shape: process }
+36 --> 42
+43["bedtools getfasta"]@{ shape: process }
+18 --> 43
+37 --> 43
+44["Regex Find And Replace"]@{ shape: process }
+38 --> 44
+45["Multi-Join"]@{ shape: process }
+40 --> 45
+39 --> 45
+46["Heatmap w ggplot"]@{ shape: process }
+41 --> 46
+47["Filter empty datasets"]@{ shape: process }
+42 --> 47
+48["ClustalW"]@{ shape: process }
+43 --> 48
+49["Filter empty datasets"]@{ shape: process }
+44 --> 49
+50["Replace Text"]@{ shape: process }
+45 --> 50
+51["FASTA-to-Tabular"]@{ shape: process }
+47 --> 51
+52["Filter empty datasets"]@{ shape: process }
+48 --> 52
+53["FASTA-to-Tabular"]@{ shape: process }
+49 --> 53
+54["Cut"]@{ shape: process }
+51 --> 54
+55["FASTTREE"]@{ shape: process }
+52 --> 55
+56["Cut"]@{ shape: process }
+53 --> 56
+57["Group"]@{ shape: process }
+54 --> 57
+58["Newick Display"]@{ shape: process }
+55 --> 58
+59["Group"]@{ shape: process }
+56 --> 59
+60["Tabular-to-FASTA"]@{ shape: process }
+57 --> 60
+61["Tabular-to-FASTA"]@{ shape: process }
+59 --> 61
+62["FASTA Merge Files and Filter Unique Sequences"]@{ shape: process }
+60 --> 62
+63["FASTA Merge Files and Filter Unique Sequences"]@{ shape: process }
+61 --> 63
+64["ClustalW"]@{ shape: process }
+62 --> 64
+65["ClustalW"]@{ shape: process }
+63 --> 65
+66["FASTTREE"]@{ shape: process }
+64 --> 66
+67["FASTTREE"]@{ shape: process }
+65 --> 67
+68["Newick Display"]@{ shape: process }
+66 --> 68
+69["Newick Display"]@{ shape: process }
+67 --> 69
+```
diff --git a/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/Taxonomy-Profiling-and-Visualization-with-Krona_diagrams.md b/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/Taxonomy-Profiling-and-Visualization-with-Krona_diagrams.md
new file mode 100644
index 000000000..8c1c08410
--- /dev/null
+++ b/workflows/microbiome/taxonomy-profiling-and-visualization-with-krona/Taxonomy-Profiling-and-Visualization-with-Krona_diagrams.md
@@ -0,0 +1,16 @@
+# Workflow diagrams
+
+## Taxonomy Profiling and Visualization with Krona
+
+```mermaid
+graph LR
+0["collection_of_preprocessed_samples"]@{ shape: docs }
+1["kraken_database"]@{ shape: lean-l }
+2["Kraken2"]@{ shape: process }
+1 --> 2
+0 --> 2
+3["Krakentools: Convert kraken report file"]@{ shape: process }
+2 --> 3
+4["Krona pie chart"]@{ shape: process }
+3 --> 4
+```
diff --git a/workflows/proteomics/clinicalmp/clinicalmp-data-interpretation/WF5_Data_Interpretation_Worklow_diagrams.md b/workflows/proteomics/clinicalmp/clinicalmp-data-interpretation/WF5_Data_Interpretation_Worklow_diagrams.md
new file mode 100644
index 000000000..7f938bf4e
--- /dev/null
+++ b/workflows/proteomics/clinicalmp/clinicalmp-data-interpretation/WF5_Data_Interpretation_Worklow_diagrams.md
@@ -0,0 +1,30 @@
+# Workflow diagrams
+
+## Clinical Metaproteomics Data Interpretation
+
+```mermaid
+graph LR
+0["Quantified Peptides"]@{ shape: doc }
+1["MaxQuant Protein Groups"]@{ shape: doc }
+2["MaxQuant Evidence"]@{ shape: doc }
+3["Annotation"]@{ shape: doc }
+4["Comparison Matrix"]@{ shape: doc }
+5["Unipept"]@{ shape: process }
+0 --> 5
+6["Microbial Proteins"]@{ shape: process }
+1 --> 6
+7["Select"]@{ shape: process }
+1 --> 7
+8["MSstatsTMT_for_microbial_proteins"]@{ shape: process }
+4 --> 8
+3 --> 8
+2 --> 8
+6 --> 8
+9["Human Proteins"]@{ shape: process }
+7 --> 9
+10["MSstatsTMT_for_human_proteins"]@{ shape: process }
+4 --> 10
+3 --> 10
+2 --> 10
+9 --> 10
+```
diff --git a/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation_diagrams.md b/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation_diagrams.md
new file mode 100644
index 000000000..763680b32
--- /dev/null
+++ b/workflows/proteomics/clinicalmp/clinicalmp-database-generation/iwc-clinicalmp-database-generation_diagrams.md
@@ -0,0 +1,22 @@
+# Workflow diagrams
+
+## Generate a Clinical Metaproteomics Database
+
+```mermaid
+graph LR
+0["Human SwissProt Protein Database"]@{ shape: doc }
+1["Tandem Mass Spectrometry (MS/MS) datasets"]@{ shape: docs }
+2["Species UniProt Protein Database"]@{ shape: doc }
+3["Contaminants cRAP Protein Database"]@{ shape: doc }
+4["Human UniProt Microbial Proteins cRAP for MetaNovo"]@{ shape: process }
+0 --> 4
+2 --> 4
+3 --> 4
+5["Metanovo"]@{ shape: process }
+4 --> 5
+1 --> 5
+6["Merge all FASTA"]@{ shape: process }
+0 --> 6
+5 --> 6
+3 --> 6
+```
diff --git a/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation_diagrams.md b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation_diagrams.md
new file mode 100644
index 000000000..7f198ce72
--- /dev/null
+++ b/workflows/proteomics/clinicalmp/clinicalmp-quantitation/iwc-clinicalmp-quantitation_diagrams.md
@@ -0,0 +1,26 @@
+# Workflow diagrams
+
+## Clinical Metaproteomics Quantitation
+
+```mermaid
+graph LR
+0["Quantitation_Database-For-MaxQuant"]@{ shape: doc }
+1["Experimental-Design Discovery MaxQuant"]@{ shape: doc }
+2["Input Raw-files"]@{ shape: docs }
+3["MaxQuant"]@{ shape: process }
+0 --> 3
+2 --> 3
+1 --> 3
+4["extracting microbial Proteins"]@{ shape: process }
+3 --> 4
+5["extracting microbial Peptides"]@{ shape: process }
+3 --> 5
+6["extract proteins"]@{ shape: process }
+4 --> 6
+7["extract peptides"]@{ shape: process }
+5 --> 7
+8["Quantified-Proteins"]@{ shape: process }
+6 --> 8
+9["Quantified-Peptides"]@{ shape: process }
+7 --> 9
+```
diff --git a/workflows/proteomics/clinicalmp/clinicalmp-verification/clinicalmp-verification_diagrams.md b/workflows/proteomics/clinicalmp/clinicalmp-verification/clinicalmp-verification_diagrams.md
new file mode 100644
index 000000000..9e52396c6
--- /dev/null
+++ b/workflows/proteomics/clinicalmp/clinicalmp-verification/clinicalmp-verification_diagrams.md
@@ -0,0 +1,52 @@
+# Workflow diagrams
+
+## Clinical Metaproteomics Verification Workflow
+
+```mermaid
+graph LR
+0["Human UniProt Isoforms FASTA"]@{ shape: process }
+1["cRAP"]@{ shape: process }
+2["Tandem Mass Spectrometry (MS/MS) datasets"]@{ shape: docs }
+3["SGPS peptide report"]@{ shape: doc }
+4["Distinct Peptides for PepQuery"]@{ shape: doc }
+5["MaxQuant peptide report"]@{ shape: doc }
+6["Human UniProt Isoforms cRAP FASTA"]@{ shape: process }
+0 --> 6
+1 --> 6
+7["SGPS Cut"]@{ shape: process }
+3 --> 7
+8["MQ Cut"]@{ shape: process }
+5 --> 8
+9["PepQuery2"]@{ shape: process }
+6 --> 9
+4 --> 9
+2 --> 9
+10["SGPS Remove Beginner"]@{ shape: process }
+7 --> 10
+11["MQ Remove Beginner"]@{ shape: process }
+8 --> 11
+12["Collapse Collection"]@{ shape: process }
+9 --> 12
+13["Concatenate datasets"]@{ shape: process }
+14["Filter"]@{ shape: process }
+12 --> 14
+15["Filter Remove beginning"]@{ shape: process }
+14 --> 15
+16["FRB Cut"]@{ shape: process }
+15 --> 16
+17["Peptide and Protein from Peptide Reports"]@{ shape: process }
+16 --> 17
+13 --> 17
+18["PPPR Remove beginning"]@{ shape: process }
+17 --> 18
+19["Group"]@{ shape: process }
+18 --> 19
+20["Uniprot ID from verified Peptides"]@{ shape: process }
+19 --> 20
+21["UniProt"]@{ shape: process }
+20 --> 21
+22["Quantitation Database for MaxQuant"]@{ shape: process }
+0 --> 22
+1 --> 22
+21 --> 22
+```
diff --git a/workflows/proteomics/openms-metaprosip/metaprosip_diagrams.md b/workflows/proteomics/openms-metaprosip/metaprosip_diagrams.md
new file mode 100644
index 000000000..fed16bdf6
--- /dev/null
+++ b/workflows/proteomics/openms-metaprosip/metaprosip_diagrams.md
@@ -0,0 +1,39 @@
+# Workflow diagrams
+
+## MetaProSIP OpenMS 2.8
+
+```mermaid
+graph LR
+0["Centroided LC-MS datasets"]@{ shape: docs }
+1["Fasta Database"]@{ shape: doc }
+2["Precursor monoisotopic mass tolerance (ppm)"]@{ shape: lean-l }
+3["Fixed modifications"]@{ shape: lean-l }
+4["Variable modifications"]@{ shape: lean-l }
+5["Labeled element"]@{ shape: lean-l }
+6["Sort collection"]@{ shape: process }
+0 --> 6
+7["DecoyDatabase"]@{ shape: process }
+1 --> 7
+8["FeatureFinderMultiplex"]@{ shape: process }
+6 --> 8
+9["MSGFPlusAdapter"]@{ shape: process }
+7 --> 9
+3 --> 9
+6 --> 9
+2 --> 9
+4 --> 9
+10["PeptideIndexer"]@{ shape: process }
+7 --> 10
+9 --> 10
+11["FalseDiscoveryRate"]@{ shape: process }
+10 --> 11
+12["IDMapper"]@{ shape: process }
+11 --> 12
+8 --> 12
+13["MetaProSIP"]@{ shape: process }
+7 --> 13
+12 --> 13
+6 --> 13
+5 --> 13
+2 --> 13
+```
diff --git a/workflows/repeatmasking/RepeatMasking-Workflow_diagrams.md b/workflows/repeatmasking/RepeatMasking-Workflow_diagrams.md
new file mode 100644
index 000000000..dcc14a197
--- /dev/null
+++ b/workflows/repeatmasking/RepeatMasking-Workflow_diagrams.md
@@ -0,0 +1,12 @@
+# Workflow diagrams
+
+## Repeat masking with RepeatModeler and RepeatMasker
+
+```mermaid
+graph LR
+0["input"]@{ shape: doc }
+1["RepeatModeler"]@{ shape: process }
+0 --> 1
+2["RepeatMasker"]@{ shape: process }
+1 --> 2
+```
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation_diagrams.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation_diagrams.md
new file mode 100644
index 000000000..7d2b47b76
--- /dev/null
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-consensus-from-variation/consensus-from-variation_diagrams.md
@@ -0,0 +1,55 @@
+# Workflow diagrams
+
+## COVID-19: consensus construction
+
+```mermaid
+graph LR
+0["Variant calls"]@{ shape: docs }
+1["min-AF for consensus variant"]@{ shape: lean-l }
+2["min-AF for failed variants"]@{ shape: lean-l }
+3["aligned reads data for depth calculation"]@{ shape: docs }
+4["Depth-threshold for masking"]@{ shape: lean-l }
+5["Reference genome"]@{ shape: doc }
+6["Compose text parameter value"]@{ shape: process }
+1 --> 6
+7["Compose text parameter value"]@{ shape: process }
+2 --> 7
+1 --> 7
+8["bedtools Genome Coverage"]@{ shape: process }
+3 --> 8
+9["Compose text parameter value"]@{ shape: process }
+4 --> 9
+10["SnpSift Filter"]@{ shape: process }
+6 --> 10
+0 --> 10
+11["SnpSift Filter"]@{ shape: process }
+7 --> 11
+0 --> 11
+12["Filter"]@{ shape: process }
+9 --> 12
+8 --> 12
+13["SnpSift Extract Fields"]@{ shape: process }
+10 --> 13
+14["SnpSift Extract Fields"]@{ shape: process }
+11 --> 14
+15["Compute"]@{ shape: process }
+13 --> 15
+16["Compute"]@{ shape: process }
+14 --> 16
+17["Concatenate"]@{ shape: process }
+12 --> 17
+16 --> 17
+18["Merge"]@{ shape: process }
+17 --> 18
+19["Subtract"]@{ shape: process }
+18 --> 19
+15 --> 19
+20["Compute"]@{ shape: process }
+19 --> 20
+21["bcftools consensus"]@{ shape: process }
+10 --> 21
+5 --> 21
+20 --> 21
+22["Collapse Collection"]@{ shape: process }
+21 --> 22
+```
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-ont-artic-variant-calling/ont-artic-variation_diagrams.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-ont-artic-variant-calling/ont-artic-variation_diagrams.md
new file mode 100644
index 000000000..11c297f2b
--- /dev/null
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-ont-artic-variant-calling/ont-artic-variation_diagrams.md
@@ -0,0 +1,69 @@
+# Workflow diagrams
+
+## COVID-19: variation analysis of ARTIC ONT data
+
+```mermaid
+graph LR
+0["ONT-sequenced reads"]@{ shape: docs }
+1["Minimum read length"]@{ shape: lean-l }
+2["Maximum read length"]@{ shape: lean-l }
+3["NC_045512.2 FASTA sequence of SARS-CoV-2"]@{ shape: doc }
+4["Primer binding sites info in BED format"]@{ shape: doc }
+5["fastp"]@{ shape: process }
+2 --> 5
+1 --> 5
+0 --> 5
+6["Compute"]@{ shape: process }
+4 --> 6
+7["Replace Text"]@{ shape: process }
+4 --> 7
+8["Map with minimap2"]@{ shape: process }
+5 --> 8
+3 --> 8
+9["Datamash"]@{ shape: process }
+6 --> 9
+10["Samtools view"]@{ shape: process }
+8 --> 10
+11["Parse parameter value"]@{ shape: process }
+9 --> 11
+12["Samtools stats"]@{ shape: process }
+10 --> 12
+13["BamLeftAlign"]@{ shape: process }
+10 --> 13
+3 --> 13
+14["ivar trim"]@{ shape: process }
+13 --> 14
+4 --> 14
+15["QualiMap BamQC"]@{ shape: process }
+14 --> 15
+16["medaka consensus tool"]@{ shape: process }
+14 --> 16
+17["Filter failed"]@{ shape: process }
+15 --> 17
+18["medaka variant tool"]@{ shape: process }
+13 --> 18
+16 --> 18
+3 --> 18
+19["medaka variant tool"]@{ shape: process }
+13 --> 19
+11 --> 19
+16 --> 19
+3 --> 19
+20["Flatten Collection"]@{ shape: process }
+17 --> 20
+21["bedtools Intersect intervals"]@{ shape: process }
+19 --> 21
+7 --> 21
+22["MultiQC"]@{ shape: process }
+12 --> 22
+20 --> 22
+23["bcftools annotate"]@{ shape: process }
+18 --> 23
+21 --> 23
+24["SnpEff eff covid19 version"]@{ shape: process }
+23 --> 24
+25["Lofreq filter"]@{ shape: process }
+24 --> 25
+26["Replace"]@{ shape: process }
+25 --> 26
+```
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis_diagrams.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis_diagrams.md
new file mode 100644
index 000000000..56cdf4338
--- /dev/null
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-ivar-analysis/pe-wgs-ivar-analysis_diagrams.md
@@ -0,0 +1,53 @@
+# Workflow diagrams
+
+## SARS-CoV-2 Illumina Amplicon pipeline - iVar based
+
+```mermaid
+graph LR
+0["Paired read collection for samples"]@{ shape: docs }
+1["Reference FASTA"]@{ shape: doc }
+2["Primer BED"]@{ shape: doc }
+3["Read fraction to call variant"]@{ shape: lean-l }
+4["Minimum quality score to call base"]@{ shape: lean-l }
+5["fastp: Trimmed Illumina Reads"]@{ shape: process }
+0 --> 5
+6["Rename reference to NC_045512.2"]@{ shape: process }
+1 --> 6
+7["Map with BWA-MEM"]@{ shape: process }
+5 --> 7
+6 --> 7
+8["Samtools stats"]@{ shape: process }
+7 --> 8
+9["Samtools view"]@{ shape: process }
+7 --> 9
+10["QualiMap BamQC"]@{ shape: process }
+9 --> 10
+11["ivar trim"]@{ shape: process }
+9 --> 11
+2 --> 11
+12["Flatten collection"]@{ shape: process }
+10 --> 12
+13["ivar variants"]@{ shape: process }
+11 --> 13
+3 --> 13
+4 --> 13
+1 --> 13
+14["ivar consensus"]@{ shape: process }
+11 --> 14
+3 --> 14
+4 --> 14
+15["Quality Control Report"]@{ shape: process }
+5 --> 15
+8 --> 15
+12 --> 15
+16["Annotated variants"]@{ shape: process }
+13 --> 16
+17["Consensus genome (masked for depth)"]@{ shape: process }
+14 --> 17
+18["Concatenate datasets"]@{ shape: process }
+17 --> 18
+19["Pangolin"]@{ shape: process }
+18 --> 19
+20["Nextclade"]@{ shape: process }
+18 --> 20
+```
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation_diagrams.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation_diagrams.md
new file mode 100644
index 000000000..4f515d4d6
--- /dev/null
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-artic-variant-calling/pe-artic-variation_diagrams.md
@@ -0,0 +1,86 @@
+# Workflow diagrams
+
+## COVID-19: variation analysis on ARTIC PE data
+
+```mermaid
+graph LR
+0["Paired Collection"]@{ shape: docs }
+1["NC_045512.2 FASTA sequence of SARS-CoV-2"]@{ shape: doc }
+2["ARTIC primer BED"]@{ shape: doc }
+3["ARTIC primers to amplicon assignments"]@{ shape: doc }
+4["Read removal minimum AF"]@{ shape: lean-l }
+5["Read removal maximum AF"]@{ shape: lean-l }
+6["Minimum DP required after amplicon bias correction"]@{ shape: lean-l }
+7["Minimum DP_ALT required after amplicon bias correction"]@{ shape: lean-l }
+8["fastp"]@{ shape: process }
+0 --> 8
+9["Compose text parameter value"]@{ shape: process }
+4 --> 9
+5 --> 9
+10["Compose text parameter value"]@{ shape: process }
+6 --> 10
+7 --> 10
+11["Map with BWA-MEM"]@{ shape: process }
+8 --> 11
+1 --> 11
+12["Samtools view"]@{ shape: process }
+11 --> 12
+13["Realign reads"]@{ shape: process }
+12 --> 13
+1 --> 13
+14["Samtools stats"]@{ shape: process }
+12 --> 14
+15["Insert indel qualities"]@{ shape: process }
+13 --> 15
+1 --> 15
+16["ivar trim"]@{ shape: process }
+3 --> 16
+15 --> 16
+2 --> 16
+17["Call variants"]@{ shape: process }
+16 --> 17
+1 --> 17
+18["QualiMap BamQC"]@{ shape: process }
+16 --> 18
+19["SnpSift Filter"]@{ shape: process }
+9 --> 19
+17 --> 19
+20["SnpSift Filter"]@{ shape: process }
+10 --> 20
+17 --> 20
+21["Filter failed datasets"]@{ shape: process }
+18 --> 21
+22["ivar removereads"]@{ shape: process }
+3 --> 22
+16 --> 22
+2 --> 22
+19 --> 22
+23["Flatten collection"]@{ shape: process }
+21 --> 23
+24["Call variants"]@{ shape: process }
+22 --> 24
+1 --> 24
+25["MultiQC"]@{ shape: process }
+8 --> 25
+14 --> 25
+23 --> 25
+26["bcftools annotate"]@{ shape: process }
+17 --> 26
+24 --> 26
+27["SnpSift Filter"]@{ shape: process }
+10 --> 27
+24 --> 27
+28["VCF-VCFintersect:"]@{ shape: process }
+1 --> 28
+27 --> 28
+20 --> 28
+29["bcftools annotate"]@{ shape: process }
+26 --> 29
+28 --> 29
+30["Replace Text"]@{ shape: process }
+29 --> 30
+31["SnpEff eff covid19 version"]@{ shape: process }
+30 --> 31
+32["Lofreq filter"]@{ shape: process }
+31 --> 32
+```
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation_diagrams.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation_diagrams.md
new file mode 100644
index 000000000..e9d1ca72d
--- /dev/null
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-pe-illumina-wgs-variant-calling/pe-wgs-variation_diagrams.md
@@ -0,0 +1,37 @@
+# Workflow diagrams
+
+## COVID-19: variation analysis on WGS PE data
+
+```mermaid
+graph LR
+0["Paired Collection"]@{ shape: docs }
+1["NC_045512.2 FASTA sequence of SARS-CoV-2"]@{ shape: doc }
+2["fastp"]@{ shape: process }
+0 --> 2
+3["Map with BWA-MEM"]@{ shape: process }
+2 --> 3
+1 --> 3
+4["Samtools view"]@{ shape: process }
+3 --> 4
+5["Samtools stats"]@{ shape: process }
+4 --> 5
+6["MarkDuplicates"]@{ shape: process }
+4 --> 6
+7["Realign reads"]@{ shape: process }
+6 --> 7
+1 --> 7
+8["MultiQC"]@{ shape: process }
+2 --> 8
+5 --> 8
+6 --> 8
+9["Insert indel qualities"]@{ shape: process }
+7 --> 9
+1 --> 9
+10["Call variants"]@{ shape: process }
+9 --> 10
+1 --> 10
+11["Lofreq filter"]@{ shape: process }
+10 --> 11
+12["SnpEff eff covid19 version"]@{ shape: process }
+11 --> 12
+```
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation_diagrams.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation_diagrams.md
new file mode 100644
index 000000000..0a66bb6e1
--- /dev/null
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-se-illumina-wgs-variant-calling/se-wgs-variation_diagrams.md
@@ -0,0 +1,33 @@
+# Workflow diagrams
+
+## COVID-19: variation analysis on WGS SE data
+
+```mermaid
+graph LR
+0["Single End Collection"]@{ shape: docs }
+1["NC_045512.2 FASTA sequence of SARS-CoV-2"]@{ shape: doc }
+2["fastp"]@{ shape: process }
+0 --> 2
+3["Bowtie2"]@{ shape: process }
+2 --> 3
+1 --> 3
+4["MarkDuplicates"]@{ shape: process }
+3 --> 4
+5["MultiQC"]@{ shape: process }
+2 --> 5
+3 --> 5
+4 --> 5
+6["Realign reads"]@{ shape: process }
+4 --> 6
+1 --> 6
+7["Insert indel qualities"]@{ shape: process }
+6 --> 7
+1 --> 7
+8["Call variants"]@{ shape: process }
+7 --> 8
+1 --> 8
+9["Lofreq filter"]@{ shape: process }
+8 --> 9
+10["SnpEff eff covid19 version"]@{ shape: process }
+9 --> 10
+```
diff --git a/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting_diagrams.md b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting_diagrams.md
new file mode 100644
index 000000000..4873719f6
--- /dev/null
+++ b/workflows/sars-cov-2-variant-calling/sars-cov-2-variation-reporting/variation-reporting_diagrams.md
@@ -0,0 +1,85 @@
+# Workflow diagrams
+
+## COVID-19: variation analysis reporting
+
+```mermaid
+graph LR
+0["Variation data to report"]@{ shape: docs }
+1["AF Filter"]@{ shape: lean-l }
+2["DP Filter"]@{ shape: lean-l }
+3["DP_ALT Filter"]@{ shape: lean-l }
+4["gene products translations"]@{ shape: doc }
+5["Number of Clusters"]@{ shape: lean-l }
+6["SnpSift Filter"]@{ shape: process }
+0 --> 6
+7["Compose text parameter value"]@{ shape: process }
+1 --> 7
+2 --> 7
+3 --> 7
+8["Compose text parameter value"]@{ shape: process }
+1 --> 8
+2 --> 8
+3 --> 8
+9["SnpSift Filter"]@{ shape: process }
+7 --> 9
+8 --> 9
+6 --> 9
+10["SnpSift Extract Fields"]@{ shape: process }
+9 --> 10
+11["Replace column"]@{ shape: process }
+10 --> 11
+4 --> 11
+12["Compute"]@{ shape: process }
+11 --> 12
+13["Datamash"]@{ shape: process }
+12 --> 13
+14["Replace"]@{ shape: process }
+13 --> 14
+15["Collapse Collection"]@{ shape: process }
+14 --> 15
+16["Compute"]@{ shape: process }
+15 --> 16
+17["Replace"]@{ shape: process }
+16 --> 17
+18["Datamash"]@{ shape: process }
+17 --> 18
+19["Filter"]@{ shape: process }
+17 --> 19
+20["Datamash"]@{ shape: process }
+17 --> 20
+21["Join"]@{ shape: process }
+19 --> 21
+18 --> 21
+22["Datamash"]@{ shape: process }
+19 --> 22
+23["Datamash"]@{ shape: process }
+19 --> 23
+24["Datamash"]@{ shape: process }
+21 --> 24
+25["Join"]@{ shape: process }
+17 --> 25
+22 --> 25
+26["Join"]@{ shape: process }
+16 --> 26
+23 --> 26
+27["Cut"]@{ shape: process }
+24 --> 27
+28["Join"]@{ shape: process }
+25 --> 28
+20 --> 28
+29["Cut"]@{ shape: process }
+26 --> 29
+30["Replace"]@{ shape: process }
+27 --> 30
+31["Cut"]@{ shape: process }
+28 --> 31
+32["Split file"]@{ shape: process }
+29 --> 32
+33["Sort"]@{ shape: process }
+30 --> 33
+34["Sort"]@{ shape: process }
+31 --> 34
+35["Variant Frequency Plot"]@{ shape: process }
+5 --> 35
+32 --> 35
+```
diff --git a/workflows/scRNAseq/baredsc/baredSC-1d-logNorm_diagrams.md b/workflows/scRNAseq/baredsc/baredSC-1d-logNorm_diagrams.md
new file mode 100644
index 000000000..bf9ad1288
--- /dev/null
+++ b/workflows/scRNAseq/baredsc/baredSC-1d-logNorm_diagrams.md
@@ -0,0 +1,40 @@
+# Workflow diagrams
+
+## baredSC_1d_logNorm
+
+```mermaid
+graph LR
+0["Tabular with raw expression values"]@{ shape: doc }
+1["Gene name"]@{ shape: lean-l }
+2["Maximum value in logNorm"]@{ shape: lean-l }
+3["Maximum number of Gaussians to study"]@{ shape: lean-l }
+4["generate_param_list_one_to_number"]@{ shape: subprocess }
+3 --> 4
+5["baredSC"]@{ shape: process }
+4 --> 5
+2 --> 5
+1 --> 5
+0 --> 5
+6["combine baredSC 1d"]@{ shape: process }
+5 --> 6
+2 --> 6
+1 --> 6
+0 --> 6
+```
+
+## generate_param_list_one_to_number
+
+```mermaid
+graph LR
+0["Maximum number in param output"]@{ shape: lean-l }
+1["create first tabular with good number of rows."]@{ shape: process }
+0 --> 1
+2["add column with numbers starting at 1"]@{ shape: process }
+1 --> 2
+3["retrieve numbers"]@{ shape: process }
+2 --> 3
+4["split numbers to collection"]@{ shape: process }
+3 --> 4
+5["numbers to param"]@{ shape: process }
+4 --> 5
+```
diff --git a/workflows/scRNAseq/baredsc/baredSC-2d-logNorm_diagrams.md b/workflows/scRNAseq/baredsc/baredSC-2d-logNorm_diagrams.md
new file mode 100644
index 000000000..c4691ea23
--- /dev/null
+++ b/workflows/scRNAseq/baredsc/baredSC-2d-logNorm_diagrams.md
@@ -0,0 +1,48 @@
+# Workflow diagrams
+
+## baredSC_2d_logNorm
+
+```mermaid
+graph LR
+0["Tabular with raw expression values"]@{ shape: doc }
+1["Gene name for x axis"]@{ shape: lean-l }
+2["maximum value in logNorm for x-axis"]@{ shape: lean-l }
+3["Gene name for y axis"]@{ shape: lean-l }
+4["maximum value in logNorm for y-axis"]@{ shape: lean-l }
+5["Maximum number of Gaussians to study"]@{ shape: lean-l }
+6["compute p-value"]@{ shape: lean-l }
+7["generate_param_list_one_to_number"]@{ shape: subprocess }
+5 --> 7
+8["baredSC 2d"]@{ shape: process }
+7 --> 8
+2 --> 8
+4 --> 8
+1 --> 8
+3 --> 8
+0 --> 8
+9["Combine multiple 2D Models"]@{ shape: process }
+8 --> 9
+2 --> 9
+4 --> 9
+6 --> 9
+1 --> 9
+3 --> 9
+0 --> 9
+```
+
+## generate_param_list_one_to_number
+
+```mermaid
+graph LR
+0["Maximum number in param output"]@{ shape: lean-l }
+1["create first tabular with good number of rows."]@{ shape: process }
+0 --> 1
+2["add column with numbers starting at 1"]@{ shape: process }
+1 --> 2
+3["retrieve numbers"]@{ shape: process }
+2 --> 3
+4["split numbers to collection"]@{ shape: process }
+3 --> 4
+5["numbers to param"]@{ shape: process }
+4 --> 5
+```
diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex_diagrams.md b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex_diagrams.md
new file mode 100644
index 000000000..bbea1ae4b
--- /dev/null
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-cellplex_diagrams.md
@@ -0,0 +1,96 @@
+# Workflow diagrams
+
+## scRNA-seq_preprocessing_10X_cellPlex
+
+```mermaid
+graph LR
+0["fastq PE collection GEX"]@{ shape: docs }
+1["reference genome"]@{ shape: lean-l }
+2["gtf"]@{ shape: doc }
+3["cellranger_barcodes_3M-february-2018.txt"]@{ shape: doc }
+4["Barcode Size is same size of the Read"]@{ shape: lean-l }
+5["fastq PE collection CMO"]@{ shape: docs }
+6["sample name and CMO sequence collection"]@{ shape: docs }
+7["Number of expected cells"]@{ shape: lean-l }
+8["process GEX reads"]@{ shape: subprocess }
+4 --> 8
+3 --> 8
+0 --> 8
+2 --> 8
+1 --> 8
+9["CITE-seq-Count"]@{ shape: process }
+7 --> 9
+5 --> 9
+6 --> 9
+3 --> 9
+10["Rename STAR-solo output"]@{ shape: process }
+8 --> 10
+11["translate 10x barcode v2 to 10x barcode v1"]@{ shape: process }
+9 --> 11
+12["Re-organize CITE-seq-Count output"]@{ shape: subprocess }
+11 --> 12
+9 --> 12
+9 --> 12
+13["rename CITE-seq output"]@{ shape: process }
+12 --> 13
+```
+
+## scRNA-seq_preprocessing_10X_v3_Bundle
+
+```mermaid
+graph LR
+0["fastq PE collection"]@{ shape: docs }
+1["reference genome"]@{ shape: lean-l }
+2["gtf"]@{ shape: doc }
+3["cellranger_barcodes_3M-february-2018.txt"]@{ shape: doc }
+4["Barcode Size is same size of the Read"]@{ shape: lean-l }
+5["RNA STARSolo"]@{ shape: process }
+1 --> 5
+2 --> 5
+0 --> 5
+4 --> 5
+3 --> 5
+6["multiQC"]@{ shape: process }
+5 --> 6
+5 --> 6
+7["filter cells"]@{ shape: process }
+5 --> 7
+5 --> 7
+5 --> 7
+8["Re-organize STAR-solo output"]@{ shape: subprocess }
+7 --> 8
+7 --> 8
+7 --> 8
+```
+
+## Re-organize-STAR-solo-output
+
+```mermaid
+graph LR
+0["STARsolo Genes"]@{ shape: docs }
+1["STARsolo Barcodes"]@{ shape: docs }
+2["STARsolo Matrix Gene Counts"]@{ shape: docs }
+3["Extract element identifiers"]@{ shape: process }
+2 --> 3
+4["Replace Text"]@{ shape: process }
+3 --> 4
+5["Replace Text"]@{ shape: process }
+3 --> 5
+6["Replace Text"]@{ shape: process }
+3 --> 6
+7["Relabel identifiers"]@{ shape: process }
+4 --> 7
+0 --> 7
+8["Relabel identifiers"]@{ shape: process }
+5 --> 8
+1 --> 8
+9["Relabel identifiers"]@{ shape: process }
+6 --> 9
+2 --> 9
+10["Merge collections"]@{ shape: process }
+9 --> 10
+8 --> 10
+7 --> 10
+11["Apply rules"]@{ shape: process }
+10 --> 11
+```
diff --git a/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3_diagrams.md b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3_diagrams.md
new file mode 100644
index 000000000..34b6e30dc
--- /dev/null
+++ b/workflows/scRNAseq/fastq-to-matrix-10x/scrna-seq-fastq-to-matrix-10x-v3_diagrams.md
@@ -0,0 +1,61 @@
+# Workflow diagrams
+
+## scRNA-seq_preprocessing_10X_v3_Bundle
+
+```mermaid
+graph LR
+0["fastq PE collection"]@{ shape: docs }
+1["reference genome"]@{ shape: lean-l }
+2["gtf"]@{ shape: doc }
+3["cellranger_barcodes_3M-february-2018.txt"]@{ shape: doc }
+4["Barcode Size is same size of the Read"]@{ shape: lean-l }
+5["RNA STARSolo"]@{ shape: process }
+1 --> 5
+2 --> 5
+0 --> 5
+4 --> 5
+3 --> 5
+6["multiQC"]@{ shape: process }
+5 --> 6
+5 --> 6
+7["filter cells"]@{ shape: process }
+5 --> 7
+5 --> 7
+5 --> 7
+8["Re-organize STAR-solo output"]@{ shape: subprocess }
+7 --> 8
+7 --> 8
+7 --> 8
+```
+
+## Re-organize-STAR-solo-output
+
+```mermaid
+graph LR
+0["STARsolo Genes"]@{ shape: docs }
+1["STARsolo Barcodes"]@{ shape: docs }
+2["STARsolo Matrix Gene Counts"]@{ shape: docs }
+3["Extract element identifiers"]@{ shape: process }
+2 --> 3
+4["Replace Text"]@{ shape: process }
+3 --> 4
+5["Replace Text"]@{ shape: process }
+3 --> 5
+6["Replace Text"]@{ shape: process }
+3 --> 6
+7["Relabel identifiers"]@{ shape: process }
+4 --> 7
+0 --> 7
+8["Relabel identifiers"]@{ shape: process }
+5 --> 8
+1 --> 8
+9["Relabel identifiers"]@{ shape: process }
+6 --> 9
+2 --> 9
+10["Merge collections"]@{ shape: process }
+9 --> 10
+8 --> 10
+7 --> 10
+11["Apply rules"]@{ shape: process }
+10 --> 11
+```
diff --git a/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/pseudo-bulk_edgeR_diagrams.md b/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/pseudo-bulk_edgeR_diagrams.md
new file mode 100644
index 000000000..5f1b6dfc8
--- /dev/null
+++ b/workflows/scRNAseq/pseudobulk-worflow-decoupler-edger/pseudo-bulk_edgeR_diagrams.md
@@ -0,0 +1,52 @@
+# Workflow diagrams
+
+## Differential gene expression for single-cell data using pseudo-bulk counts with edgeR
+
+```mermaid
+graph LR
+0["Source AnnData file"]@{ shape: doc }
+1["Pseudo-bulk: Fields to merge"]@{ shape: lean-l }
+2["Group by column"]@{ shape: lean-l }
+3["Sample key column"]@{ shape: lean-l }
+4["Name Your Raw Counts Layer"]@{ shape: lean-l }
+5["Factor fields"]@{ shape: lean-l }
+6["Formula"]@{ shape: lean-l }
+7["Gene symbol column"]@{ shape: lean-l }
+8["Decoupler pseudo-bulk"]@{ shape: process }
+1 --> 8
+5 --> 8
+2 --> 8
+0 --> 8
+4 --> 8
+3 --> 8
+9["Sanitize matrix"]@{ shape: process }
+8 --> 9
+10["Sanitize factors"]@{ shape: process }
+8 --> 10
+11["Remove start, end, width"]@{ shape: process }
+8 --> 11
+12["Sanitize first factor for leading digits"]@{ shape: process }
+10 --> 12
+13["Text reformatting"]@{ shape: process }
+12 --> 13
+14["edgeR"]@{ shape: process }
+11 --> 14
+13 --> 14
+6 --> 14
+9 --> 14
+12 --> 14
+15["Get contrast labels"]@{ shape: process }
+14 --> 15
+16["Select gene symbols, logFC, PValue and FDR"]@{ shape: process }
+7 --> 16
+14 --> 16
+17["Replace Text"]@{ shape: process }
+15 --> 17
+18["Split contrasts"]@{ shape: process }
+17 --> 18
+19["Contrast as parameters"]@{ shape: process }
+18 --> 19
+20["Volcano Plot"]@{ shape: process }
+16 --> 20
+19 --> 20
+```
diff --git a/workflows/scRNAseq/velocyto/Velocyto-on10X-filtered-barcodes_diagrams.md b/workflows/scRNAseq/velocyto/Velocyto-on10X-filtered-barcodes_diagrams.md
new file mode 100644
index 000000000..c98ebbc41
--- /dev/null
+++ b/workflows/scRNAseq/velocyto/Velocyto-on10X-filtered-barcodes_diagrams.md
@@ -0,0 +1,14 @@
+# Workflow diagrams
+
+## Velocyto-on10X-filtered-barcodes
+
+```mermaid
+graph LR
+0["BAM files with CB and UB"]@{ shape: docs }
+1["filtered barcodes"]@{ shape: docs }
+2["gtf file"]@{ shape: doc }
+3["velocyto"]@{ shape: process }
+0 --> 3
+1 --> 3
+2 --> 3
+```
diff --git a/workflows/scRNAseq/velocyto/Velocyto-on10X-from-bundled_diagrams.md b/workflows/scRNAseq/velocyto/Velocyto-on10X-from-bundled_diagrams.md
new file mode 100644
index 000000000..246250616
--- /dev/null
+++ b/workflows/scRNAseq/velocyto/Velocyto-on10X-from-bundled_diagrams.md
@@ -0,0 +1,29 @@
+# Workflow diagrams
+
+## Velocyto-on10X-from-bundled
+
+```mermaid
+graph LR
+0["BAM files with CB and UB"]@{ shape: docs }
+1["filtered matrices in bundle"]@{ shape: docs }
+2["gtf file"]@{ shape: doc }
+3["extract barcodes from bundle"]@{ shape: process }
+1 --> 3
+4["Velocyto_on10X_filtered_barcodes"]@{ shape: subprocess }
+0 --> 4
+3 --> 4
+2 --> 4
+```
+
+## Velocyto_on10X_filtered_barcodes
+
+```mermaid
+graph LR
+0["BAM files with CB and UB"]@{ shape: docs }
+1["filtered barcodes"]@{ shape: docs }
+2["gtf file"]@{ shape: doc }
+3["velocyto"]@{ shape: process }
+0 --> 3
+1 --> 3
+2 --> 3
+```
diff --git a/workflows/transcriptomics/brew3r/BREW3R_diagrams.md b/workflows/transcriptomics/brew3r/BREW3R_diagrams.md
new file mode 100644
index 000000000..8b7de4c8f
--- /dev/null
+++ b/workflows/transcriptomics/brew3r/BREW3R_diagrams.md
@@ -0,0 +1,28 @@
+# Workflow diagrams
+
+## BREW3R
+
+```mermaid
+graph LR
+0["Input gtf"]@{ shape: doc }
+1["BAM collection"]@{ shape: docs }
+2["strandedness"]@{ shape: lean-l }
+3["minimum coverage"]@{ shape: lean-l }
+4["minimum FPKM for merge"]@{ shape: lean-l }
+5["Map parameter value"]@{ shape: process }
+2 --> 5
+6["Unstranded"]@{ shape: process }
+2 --> 6
+7["assembl with StringTie"]@{ shape: process }
+3 --> 7
+3 --> 7
+1 --> 7
+5 --> 7
+8["merge assembled transcripts"]@{ shape: process }
+7 --> 8
+4 --> 8
+9["BREW3R.r"]@{ shape: process }
+6 --> 9
+0 --> 9
+8 --> 9
+```
diff --git a/workflows/transcriptomics/goseq/goseq-go-kegg-enrichment-analsis_diagrams.md b/workflows/transcriptomics/goseq/goseq-go-kegg-enrichment-analsis_diagrams.md
new file mode 100644
index 000000000..8f77becfa
--- /dev/null
+++ b/workflows/transcriptomics/goseq/goseq-go-kegg-enrichment-analsis_diagrams.md
@@ -0,0 +1,35 @@
+# Workflow diagrams
+
+## Goseq GO-KEGG Enrichment Analysis
+
+```mermaid
+graph LR
+0["Select genome to use"]@{ shape: lean-l }
+1["Differential expression result"]@{ shape: doc }
+2["Select gene ID format"]@{ shape: lean-l }
+3["gene length"]@{ shape: doc }
+4["KEGG pathways"]@{ shape: doc }
+5["goseq - Cellular Component"]@{ shape: process }
+2 --> 5
+0 --> 5
+1 --> 5
+3 --> 5
+6["goseq - Biological Process"]@{ shape: process }
+2 --> 6
+0 --> 6
+1 --> 6
+3 --> 6
+7["goseq - Molecular Function"]@{ shape: process }
+2 --> 7
+0 --> 7
+1 --> 7
+3 --> 7
+8["goseq - KEGG"]@{ shape: process }
+2 --> 8
+0 --> 8
+1 --> 8
+3 --> 8
+9["Join two Datasets"]@{ shape: process }
+8 --> 9
+4 --> 9
+```
diff --git a/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting_diagrams.md b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting_diagrams.md
new file mode 100644
index 000000000..80618cb3b
--- /dev/null
+++ b/workflows/transcriptomics/rnaseq-de/rnaseq-de-filtering-plotting_diagrams.md
@@ -0,0 +1,61 @@
+# Workflow diagrams
+
+## RNAseq_DE_filtering_plotting
+
+```mermaid
+graph LR
+0["Counts from changed condition"]@{ shape: docs }
+1["Counts from reference condition"]@{ shape: docs }
+2["Count files have header"]@{ shape: lean-l }
+3["Gene Annotaton"]@{ shape: doc }
+4["Adjusted p-value threshold"]@{ shape: lean-l }
+5["Create text file"]@{ shape: process }
+6["log2 fold change threshold"]@{ shape: lean-l }
+7["Pick parameter value"]@{ shape: process }
+4 --> 7
+8["Text transformation"]@{ shape: process }
+5 --> 8
+9["Pick parameter value"]@{ shape: process }
+6 --> 9
+10["Differential Analysis"]@{ shape: process }
+2 --> 10
+7 --> 10
+0 --> 10
+1 --> 10
+11["Compose text parameter value"]@{ shape: process }
+7 --> 11
+12["Compose text parameter value"]@{ shape: process }
+9 --> 12
+13["Annotate DESeq2/DEXSeq output tables"]@{ shape: process }
+3 --> 13
+10 --> 13
+14["Text reformatting"]@{ shape: process }
+10 --> 14
+15["Annotate DESeq2 table"]@{ shape: process }
+8 --> 15
+13 --> 15
+16["Parse parameter value"]@{ shape: process }
+14 --> 16
+17["Filter with p-adj threshold"]@{ shape: process }
+11 --> 17
+15 --> 17
+18["Generate Valcanot plot of DE genes"]@{ shape: process }
+15 --> 18
+9 --> 18
+7 --> 18
+19["Compose text parameter value"]@{ shape: process }
+16 --> 19
+20["Filter with log2 FC threshold"]@{ shape: process }
+12 --> 20
+17 --> 20
+21["Join two Datasets"]@{ shape: process }
+10 --> 21
+20 --> 21
+22["Cut"]@{ shape: process }
+19 --> 22
+21 --> 22
+23["Generate Heatmap of counts"]@{ shape: process }
+22 --> 23
+24["Generate Heatmap of Z-scores"]@{ shape: process }
+22 --> 24
+```
diff --git a/workflows/transcriptomics/rnaseq-pe/rnaseq-pe_diagrams.md b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe_diagrams.md
new file mode 100644
index 000000000..7be3f024b
--- /dev/null
+++ b/workflows/transcriptomics/rnaseq-pe/rnaseq-pe_diagrams.md
@@ -0,0 +1,196 @@
+# Workflow diagrams
+
+## RNA-seq for Paired-end fastqs
+
+```mermaid
+graph LR
+0["Collection paired FASTQ files"]@{ shape: docs }
+1["Forward adapter"]@{ shape: lean-l }
+2["Reverse adapter"]@{ shape: lean-l }
+3["Generate additional QC reports"]@{ shape: lean-l }
+4["Reference genome"]@{ shape: lean-l }
+5["GTF file of annotation"]@{ shape: doc }
+6["Strandedness"]@{ shape: lean-l }
+7["Use featureCounts for generating count tables"]@{ shape: lean-l }
+8["Compute Cufflinks FPKM"]@{ shape: lean-l }
+9["GTF with regions to exclude from FPKM normalization with Cufflinks"]@{ shape: doc }
+10["Compute StringTie FPKM"]@{ shape: lean-l }
+11["Flatten collection"]@{ shape: process }
+0 --> 11
+12["remove adapters + bad quality bases"]@{ shape: process }
+1 --> 12
+2 --> 12
+0 --> 12
+13["no additional QC"]@{ shape: process }
+3 --> 13
+14["get reference_genome as text parameter"]@{ shape: process }
+4 --> 14
+15["Get featureCounts strandedness parameter"]@{ shape: process }
+6 --> 15
+16["Get cufflinks strandedness parameter"]@{ shape: process }
+6 --> 16
+17["Get Stringtie strandedness parameter"]@{ shape: process }
+6 --> 17
+18["STAR: map and count and coverage splitted"]@{ shape: process }
+4 --> 18
+5 --> 18
+12 --> 18
+19["Generate Unstranded Coverage"]@{ shape: subprocess }
+18 --> 19
+18 --> 19
+20["Generate Stranded Coverage"]@{ shape: subprocess }
+18 --> 20
+18 --> 20
+6 --> 20
+21["featureCounts"]@{ shape: process }
+18 --> 21
+5 --> 21
+15 --> 21
+7 --> 21
+22["Compute FPKM with StringTie"]@{ shape: process }
+5 --> 22
+18 --> 22
+17 --> 22
+10 --> 22
+23["Compute FPKM with cufflinks"]@{ shape: process }
+16 --> 23
+9 --> 23
+14 --> 23
+18 --> 23
+5 --> 23
+8 --> 23
+24["Process Count files"]@{ shape: subprocess }
+18 --> 24
+6 --> 24
+21 --> 24
+21 --> 24
+25["Combined MultiQC without additional QC"]@{ shape: process }
+12 --> 25
+18 --> 25
+18 --> 25
+24 --> 25
+13 --> 25
+26["Combined MultiQC Quality Report with additional QC"]@{ shape: subprocess }
+11 --> 26
+18 --> 26
+18 --> 26
+18 --> 26
+12 --> 26
+24 --> 26
+5 --> 26
+3 --> 26
+```
+
+## RNA-seq-Paired-QC
+
+```mermaid
+graph LR
+0["FASTQ collection"]@{ shape: docs }
+1["fastp Reports"]@{ shape: docs }
+2["STAR logs"]@{ shape: docs }
+3["STAR gene counts"]@{ shape: docs }
+4["featureCounts summaries"]@{ shape: docs }
+5["reference_annotation_gtf"]@{ shape: doc }
+6["STAR paired-end BAM"]@{ shape: docs }
+7["FastQC check read qualities"]@{ shape: process }
+0 --> 7
+8["convert gtf to bed12"]@{ shape: process }
+5 --> 8
+9["Subsample 200k reads"]@{ shape: process }
+6 --> 9
+10["Get reads number per chromosome"]@{ shape: process }
+6 --> 10
+11["Remove duplicates"]@{ shape: process }
+6 --> 11
+12["Read distribution over genomic features"]@{ shape: process }
+6 --> 12
+8 --> 12
+13["Get gene body coverage"]@{ shape: process }
+9 --> 13
+8 --> 13
+14["Combined Quality Report"]@{ shape: process }
+7 --> 14
+1 --> 14
+2 --> 14
+3 --> 14
+4 --> 14
+12 --> 14
+13 --> 14
+10 --> 14
+11 --> 14
+```
+
+## Process Count files
+
+```mermaid
+graph LR
+0["A dummy featureCounts summary file"]@{ shape: process }
+1["featureCounts summaries collection"]@{ shape: docs }
+2["Strandness param"]@{ shape: lean-l }
+3["RNA STAR count tables"]@{ shape: docs }
+4["featureCounts count table"]@{ shape: docs }
+5["Text transformation"]@{ shape: process }
+0 --> 5
+6["awk command from strand for STAR counts"]@{ shape: process }
+2 --> 6
+7["featureCounts summaries"]@{ shape: process }
+1 --> 7
+5 --> 7
+8["Extract gene counts"]@{ shape: process }
+6 --> 8
+3 --> 8
+9["Counts table"]@{ shape: process }
+4 --> 9
+8 --> 9
+```
+
+## Re-arrange Stranded RNA-seq coverage
+
+```mermaid
+graph LR
+0["strandedness"]@{ shape: lean-l }
+1["Bedgraph strand 1"]@{ shape: docs }
+2["Bedgraph strand 2"]@{ shape: docs }
+3["Get replacement for strand2"]@{ shape: process }
+0 --> 3
+4["Get replacement for strand1"]@{ shape: process }
+0 --> 4
+5["get identifiers"]@{ shape: process }
+1 --> 5
+6["New labels strand 2"]@{ shape: process }
+3 --> 6
+5 --> 6
+7["New labels strand 1"]@{ shape: process }
+4 --> 7
+5 --> 7
+8["Relabelled strand 2"]@{ shape: process }
+6 --> 8
+2 --> 8
+9["Relabelled strand 1"]@{ shape: process }
+7 --> 9
+1 --> 9
+10["Merge collections"]@{ shape: process }
+9 --> 10
+8 --> 10
+11["convert to bigwig"]@{ shape: process }
+10 --> 11
+```
+
+## Get Uniquely mapped unstranded coverage
+
+```mermaid
+graph LR
+0["STAR log"]@{ shape: docs }
+1["STAR BAM"]@{ shape: docs }
+2["get scaling factor"]@{ shape: process }
+0 --> 2
+3["keep uniquely mapped reads"]@{ shape: process }
+1 --> 3
+4["Parse parameter value"]@{ shape: process }
+2 --> 4
+5["Scaled Coverage both strands combined"]@{ shape: process }
+3 --> 5
+4 --> 5
+6["convert both strands coverage to bigwig"]@{ shape: process }
+5 --> 6
+```
diff --git a/workflows/transcriptomics/rnaseq-sr/rnaseq-sr_diagrams.md b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr_diagrams.md
new file mode 100644
index 000000000..3c7ddc8f6
--- /dev/null
+++ b/workflows/transcriptomics/rnaseq-sr/rnaseq-sr_diagrams.md
@@ -0,0 +1,192 @@
+# Workflow diagrams
+
+## RNA-seq for Single-read fastqs
+
+```mermaid
+graph LR
+0["Collection of FASTQ files"]@{ shape: docs }
+1["Forward adapter"]@{ shape: lean-l }
+2["Generate additional QC reports"]@{ shape: lean-l }
+3["Reference genome"]@{ shape: lean-l }
+4["GTF file of annotation"]@{ shape: doc }
+5["Strandedness"]@{ shape: lean-l }
+6["Use featureCounts for generating count tables"]@{ shape: lean-l }
+7["Compute Cufflinks FPKM"]@{ shape: lean-l }
+8["GTF with regions to exclude from FPKM normalization with Cufflinks"]@{ shape: doc }
+9["Compute StringTie FPKM"]@{ shape: lean-l }
+10["remove adapters + bad quality bases"]@{ shape: process }
+1 --> 10
+0 --> 10
+11["no additional QC"]@{ shape: process }
+2 --> 11
+12["get reference_genome as text parameter"]@{ shape: process }
+3 --> 12
+13["Get featureCounts strandedness parameter"]@{ shape: process }
+5 --> 13
+14["Get cufflinks strandedness parameter"]@{ shape: process }
+5 --> 14
+15["Get Stringtie strandedness parameter"]@{ shape: process }
+5 --> 15
+16["STAR: map and count and coverage splitted"]@{ shape: process }
+3 --> 16
+4 --> 16
+10 --> 16
+17["Generate Unstranded Coverage"]@{ shape: subprocess }
+16 --> 17
+16 --> 17
+18["Generate Stranded Coverage"]@{ shape: subprocess }
+16 --> 18
+16 --> 18
+5 --> 18
+19["featureCounts"]@{ shape: process }
+16 --> 19
+4 --> 19
+13 --> 19
+6 --> 19
+20["Compute FPKM with StringTie"]@{ shape: process }
+4 --> 20
+16 --> 20
+15 --> 20
+9 --> 20
+21["Compute FPKM with cufflinks"]@{ shape: process }
+14 --> 21
+8 --> 21
+12 --> 21
+16 --> 21
+4 --> 21
+7 --> 21
+22["Process Count files"]@{ shape: subprocess }
+16 --> 22
+5 --> 22
+19 --> 22
+19 --> 22
+23["Combined MultiQC without additional QC"]@{ shape: process }
+10 --> 23
+16 --> 23
+16 --> 23
+22 --> 23
+11 --> 23
+24["Combined MultiQC Quality Report"]@{ shape: subprocess }
+0 --> 24
+16 --> 24
+16 --> 24
+16 --> 24
+10 --> 24
+22 --> 24
+4 --> 24
+2 --> 24
+```
+
+## RNA-seq-QC
+
+```mermaid
+graph LR
+0["FASTQ collection"]@{ shape: docs }
+1["fastp Reports"]@{ shape: docs }
+2["STAR logs"]@{ shape: docs }
+3["STAR counts"]@{ shape: docs }
+4["featureCounts summaries"]@{ shape: docs }
+5["reference_annotation_gtf"]@{ shape: doc }
+6["STAR BAM"]@{ shape: docs }
+7["FastQC check read qualities"]@{ shape: process }
+0 --> 7
+8["convert gtf to bed12"]@{ shape: process }
+5 --> 8
+9["Subsample 200k reads"]@{ shape: process }
+6 --> 9
+10["Get reads number per chromosome"]@{ shape: process }
+6 --> 10
+11["Remove duplicates"]@{ shape: process }
+6 --> 11
+12["Read distribution over genomic features"]@{ shape: process }
+6 --> 12
+8 --> 12
+13["Get gene body coverage"]@{ shape: process }
+9 --> 13
+8 --> 13
+14["Combined Quality Report"]@{ shape: process }
+7 --> 14
+1 --> 14
+2 --> 14
+3 --> 14
+4 --> 14
+12 --> 14
+13 --> 14
+10 --> 14
+11 --> 14
+```
+
+## Process Count files
+
+```mermaid
+graph LR
+0["A dummy featureCounts summary file"]@{ shape: process }
+1["featureCounts summaries collection"]@{ shape: docs }
+2["Strandness param"]@{ shape: lean-l }
+3["RNA STAR count tables"]@{ shape: docs }
+4["featureCounts count table"]@{ shape: docs }
+5["Text transformation"]@{ shape: process }
+0 --> 5
+6["awk command from strand for STAR counts"]@{ shape: process }
+2 --> 6
+7["featureCounts summaries"]@{ shape: process }
+1 --> 7
+5 --> 7
+8["Extract gene counts"]@{ shape: process }
+6 --> 8
+3 --> 8
+9["Counts table"]@{ shape: process }
+4 --> 9
+8 --> 9
+```
+
+## Re-arrange Stranded RNA-seq coverage
+
+```mermaid
+graph LR
+0["strandedness"]@{ shape: lean-l }
+1["Bedgraph strand 1"]@{ shape: docs }
+2["Bedgraph strand 2"]@{ shape: docs }
+3["Get replacement for strand2"]@{ shape: process }
+0 --> 3
+4["Get replacement for strand1"]@{ shape: process }
+0 --> 4
+5["get identifiers"]@{ shape: process }
+1 --> 5
+6["New labels strand 2"]@{ shape: process }
+3 --> 6
+5 --> 6
+7["New labels strand 1"]@{ shape: process }
+4 --> 7
+5 --> 7
+8["Relabelled strand 2"]@{ shape: process }
+6 --> 8
+2 --> 8
+9["Relabelled strand 1"]@{ shape: process }
+7 --> 9
+1 --> 9
+10["Merge collections"]@{ shape: process }
+9 --> 10
+8 --> 10
+11["convert to bigwig"]@{ shape: process }
+10 --> 11
+```
+
+## Get Uniquely mapped unstranded coverage
+
+```mermaid
+graph LR
+0["STAR log"]@{ shape: docs }
+1["STAR BAM"]@{ shape: docs }
+2["get scaling factor"]@{ shape: process }
+0 --> 2
+3["keep uniquely mapped reads"]@{ shape: process }
+1 --> 3
+4["Parse parameter value"]@{ shape: process }
+2 --> 4
+5["Scaled Coverage both strands combined"]@{ shape: process }
+3 --> 5
+4 --> 5
+6["convert both strands coverage to bigwig"]@{ shape: process }
+5 --> 6
+```
diff --git a/workflows/variant-calling/generic-variant-calling-wgs-pe/Generic-variation-analysis-on-WGS-PE-data_diagrams.md b/workflows/variant-calling/generic-variant-calling-wgs-pe/Generic-variation-analysis-on-WGS-PE-data_diagrams.md
new file mode 100644
index 000000000..d11741d7c
--- /dev/null
+++ b/workflows/variant-calling/generic-variant-calling-wgs-pe/Generic-variation-analysis-on-WGS-PE-data_diagrams.md
@@ -0,0 +1,42 @@
+# Workflow diagrams
+
+## Generic variation analysis on WGS PE data
+
+```mermaid
+graph LR
+0["Paired Collection"]@{ shape: docs }
+1["GenBank genome"]@{ shape: doc }
+2["Name for genome database"]@{ shape: lean-l }
+3["fastp"]@{ shape: process }
+0 --> 3
+4["SnpEff build:"]@{ shape: process }
+2 --> 4
+1 --> 4
+5["Map with BWA-MEM"]@{ shape: process }
+3 --> 5
+4 --> 5
+6["Samtools view"]@{ shape: process }
+5 --> 6
+7["MarkDuplicates"]@{ shape: process }
+6 --> 7
+8["Samtools stats"]@{ shape: process }
+6 --> 8
+9["Realign reads"]@{ shape: process }
+7 --> 9
+4 --> 9
+10["MultiQC"]@{ shape: process }
+3 --> 10
+8 --> 10
+7 --> 10
+11["Insert indel qualities"]@{ shape: process }
+9 --> 11
+4 --> 11
+12["Call variants"]@{ shape: process }
+11 --> 12
+4 --> 12
+13["Lofreq filter"]@{ shape: process }
+12 --> 13
+14["SnpEff eff:"]@{ shape: process }
+13 --> 14
+4 --> 14
+```
diff --git a/workflows/variant-calling/haploid-variant-calling-wgs-pe/WGS-PE-variant-calling-in-haploid-system_diagrams.md b/workflows/variant-calling/haploid-variant-calling-wgs-pe/WGS-PE-variant-calling-in-haploid-system_diagrams.md
new file mode 100644
index 000000000..a1733c44a
--- /dev/null
+++ b/workflows/variant-calling/haploid-variant-calling-wgs-pe/WGS-PE-variant-calling-in-haploid-system_diagrams.md
@@ -0,0 +1,43 @@
+# Workflow diagrams
+
+## Paired end variant calling in haploid system
+
+```mermaid
+graph LR
+0["Paired Collection"]@{ shape: docs }
+1["Annotation GTF"]@{ shape: doc }
+2["Genome fasta"]@{ shape: doc }
+3["fastp"]@{ shape: process }
+0 --> 3
+4["SnpEff build:"]@{ shape: process }
+1 --> 4
+2 --> 4
+5["Map with BWA-MEM"]@{ shape: process }
+3 --> 5
+2 --> 5
+6["Samtools view"]@{ shape: process }
+5 --> 6
+7["Samtools stats"]@{ shape: process }
+6 --> 7
+8["MarkDuplicates"]@{ shape: process }
+6 --> 8
+9["MultiQC"]@{ shape: process }
+3 --> 9
+7 --> 9
+8 --> 9
+10["Realign reads"]@{ shape: process }
+8 --> 10
+2 --> 10
+11["Call variants"]@{ shape: process }
+10 --> 11
+2 --> 11
+12["Text reformatting"]@{ shape: process }
+11 --> 12
+13["SnpEff eff:"]@{ shape: process }
+12 --> 13
+4 --> 13
+14["SnpSift Extract Fields"]@{ shape: process }
+13 --> 14
+15["Collapse Collection"]@{ shape: process }
+14 --> 15
+```
diff --git a/workflows/variant-calling/variation-reporting/Generic-variation-analysis-reporting_diagrams.md b/workflows/variant-calling/variation-reporting/Generic-variation-analysis-reporting_diagrams.md
new file mode 100644
index 000000000..76436228a
--- /dev/null
+++ b/workflows/variant-calling/variation-reporting/Generic-variation-analysis-reporting_diagrams.md
@@ -0,0 +1,83 @@
+# Workflow diagrams
+
+## Generic variation analysis reporting
+
+```mermaid
+graph LR
+0["Variation data to report"]@{ shape: docs }
+1["AF Filter"]@{ shape: lean-l }
+2["DP Filter"]@{ shape: lean-l }
+3["DP_ALT Filter"]@{ shape: lean-l }
+4["SnpSift Filter"]@{ shape: process }
+0 --> 4
+5["Compose text parameter value"]@{ shape: process }
+1 --> 5
+2 --> 5
+3 --> 5
+6["Compose text parameter value"]@{ shape: process }
+1 --> 6
+2 --> 6
+3 --> 6
+7["SnpSift Filter"]@{ shape: process }
+5 --> 7
+6 --> 7
+4 --> 7
+8["SnpSift Extract Fields"]@{ shape: process }
+7 --> 8
+9["Compute"]@{ shape: process }
+8 --> 9
+10["Datamash"]@{ shape: process }
+9 --> 10
+11["Replace"]@{ shape: process }
+10 --> 11
+12["Replace"]@{ shape: process }
+11 --> 12
+13["Replace"]@{ shape: process }
+12 --> 13
+14["Collapse Collection"]@{ shape: process }
+13 --> 14
+15["Compute"]@{ shape: process }
+14 --> 15
+16["Compute"]@{ shape: process }
+15 --> 16
+17["Replace"]@{ shape: process }
+16 --> 17
+18["Datamash"]@{ shape: process }
+17 --> 18
+19["Filter"]@{ shape: process }
+17 --> 19
+20["Datamash"]@{ shape: process }
+17 --> 20
+21["Datamash"]@{ shape: process }
+19 --> 21
+22["Join"]@{ shape: process }
+19 --> 22
+18 --> 22
+23["Datamash"]@{ shape: process }
+19 --> 23
+24["Join"]@{ shape: process }
+16 --> 24
+21 --> 24
+25["Datamash"]@{ shape: process }
+22 --> 25
+26["Join"]@{ shape: process }
+17 --> 26
+23 --> 26
+27["Cut"]@{ shape: process }
+24 --> 27
+28["Cut"]@{ shape: process }
+25 --> 28
+29["Join"]@{ shape: process }
+26 --> 29
+20 --> 29
+30["Split file"]@{ shape: process }
+27 --> 30
+31["Replace"]@{ shape: process }
+28 --> 31
+32["Cut"]@{ shape: process }
+29 --> 32
+33["Sort"]@{ shape: process }
+31 --> 33
+34["Sort"]@{ shape: process }
+32 --> 34
+```
diff --git a/workflows/virology/pox-virus-amplicon/pox-virus-half-genome_diagrams.md b/workflows/virology/pox-virus-amplicon/pox-virus-half-genome_diagrams.md
new file mode 100644
index 000000000..2bd588942
--- /dev/null
+++ b/workflows/virology/pox-virus-amplicon/pox-virus-half-genome_diagrams.md
@@ -0,0 +1,109 @@
+# Workflow diagrams
+
+## Pox Virus Illumina Amplicon Workflow from half-genomes
+
+```mermaid
+graph LR
+0["Reference FASTA"]@{ shape: doc }
+1["Primer Scheme"]@{ shape: doc }
+2["PE Reads Pool1"]@{ shape: docs }
+3["PE Reads Pool2"]@{ shape: docs }
+4["Minimum quality score to call base"]@{ shape: lean-l }
+5["Allele frequency to call SNV"]@{ shape: lean-l }
+6["Allele frequency to call indel"]@{ shape: lean-l }
+7["Compute sequence length"]@{ shape: process }
+0 --> 7
+8["Select pool1 primers"]@{ shape: process }
+1 --> 8
+9["Select pool2 primers"]@{ shape: process }
+1 --> 9
+10["Extract element identifiers"]@{ shape: process }
+2 --> 10
+11["fastp: Trimmed Illumina Reads Pool1"]@{ shape: process }
+2 --> 11
+12["Cut"]@{ shape: process }
+7 --> 12
+13["Datamash"]@{ shape: process }
+8 --> 13
+14["Datamash"]@{ shape: process }
+9 --> 14
+15["Split file"]@{ shape: process }
+10 --> 15
+16["Sort collection"]@{ shape: process }
+3 --> 16
+10 --> 16
+17["Get end position of sequence"]@{ shape: process }
+12 --> 17
+18["Get end position of Pool1"]@{ shape: process }
+13 --> 18
+19["Get start position of Pool2"]@{ shape: process }
+14 --> 19
+20["Parse parameter value"]@{ shape: process }
+15 --> 20
+21["fastp: Trimmed Illumina Reads Pool2"]@{ shape: process }
+16 --> 21
+22["Compose text parameter value"]@{ shape: process }
+18 --> 22
+17 --> 22
+23["Compose text parameter value"]@{ shape: process }
+19 --> 23
+24["Compose text parameter value"]@{ shape: process }
+20 --> 24
+25["Compose text parameter value"]@{ shape: process }
+20 --> 25
+26["Mask Reference for Pool1"]@{ shape: process }
+0 --> 26
+22 --> 26
+27["Mask Reference for Pool2"]@{ shape: process }
+0 --> 27
+23 --> 27
+28["Map with BWA-MEM"]@{ shape: process }
+11 --> 28
+26 --> 28
+24 --> 28
+29["Map with BWA-MEM"]@{ shape: process }
+21 --> 29
+27 --> 29
+25 --> 29
+30["Samtools view"]@{ shape: process }
+28 --> 30
+31["Samtools stats"]@{ shape: process }
+28 --> 31
+32["Samtools view"]@{ shape: process }
+29 --> 32
+33["Samtools stats"]@{ shape: process }
+29 --> 33
+34["MultiQC"]@{ shape: process }
+11 --> 34
+31 --> 34
+35["Zip collections"]@{ shape: process }
+30 --> 35
+32 --> 35
+36["MultiQC"]@{ shape: process }
+21 --> 36
+33 --> 36
+37["Apply rules"]@{ shape: process }
+35 --> 37
+38["Samtools merge"]@{ shape: process }
+37 --> 38
+39["QualiMap BamQC"]@{ shape: process }
+38 --> 39
+40["ivar trim"]@{ shape: process }
+38 --> 40
+1 --> 40
+41["Filter failed datasets"]@{ shape: process }
+39 --> 41
+42["ivar consensus"]@{ shape: process }
+40 --> 42
+5 --> 42
+6 --> 42
+4 --> 42
+43["Flatten collection"]@{ shape: process }
+41 --> 43
+44["Text transformation"]@{ shape: process }
+42 --> 44
+45["MultiQC"]@{ shape: process }
+43 --> 45
+46["Concatenate datasets"]@{ shape: process }
+44 --> 46
+```