Merge pull request #1138 from mahesh-panchal/dev

Update FastQC and UMItools modules
nf-core · Dec 8, 2023 · f55a154 · f55a154
2 parents f92aa38 + ed2b8aa
commit f55a154
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -10,11 +10,26 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 - [PR #1135](https://github.com/nf-core/rnaseq/pull/1135) - Update [action-tower-launch](https://github.com/marketplace/actions/action-tower-launch) to v2 which supports more variable handling.
+- [PR #1138](https://github.com/nf-core/rnaseq/pull/1138) - Updates FASTQC and UMITOOLS modules and their dependencies which have had their version string extraction commands updated ([#1103](https://github.com/nf-core/rnaseq/issues/1103))
+- Update Rseqc and Fastp modules to print STDERR to screen and file.
 
 ### Software dependencies
 
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `picard`   | 3.0.0       | 3.1.1       |
+| `samtools` | 1.17        | 1.18        |
+
+> **NB:** Dependency has been **updated** if both old and new version information is present.
+>
+> **NB:** Dependency has been **added** if just the new version information is present.
+>
+> **NB:** Dependency has been **removed** if new version information isn't present.
+
 ### Modules / Subworkflows
 
+- BAM_RSEQC subworkflow updated with new channel names.
+
 ## [[3.13.2](https://github.com/nf-core/rnaseq/releases/tag/3.13.2)] - 2023-11-21
 
 ### Credits

diff --git a/modules.json b/modules.json
@@ -27,12 +27,12 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "d497a4868ace3302016ea8ed4b395072d5e833cd",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
+                        "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
+                        "installed_by": ["modules", "fastq_fastqc_umitools_fastp"]
                     },
                     "fastqc": {
                         "branch": "master",
-                        "git_sha": "102cc9b709a6da9f7cee2373563ab1464fca9c0a",
+                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
                     },
                     "fq/subsample": {
@@ -77,7 +77,7 @@
                     },
                     "picard/markduplicates": {
                         "branch": "master",
-                        "git_sha": "2ee934606f1fdf7fc1cb05d6e8abc13bec8ab448",
+                        "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447",
                         "installed_by": ["bam_markduplicates_picard"]
                     },
                     "preseq/lcextrap": {
@@ -102,42 +102,42 @@
                     },
                     "rseqc/bamstat": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "65acf692457e8c466e104c6a3e5ac392e98fe688",
                         "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/inferexperiment": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "f2a3328fde9a2b4185285057f8d3727f39dd2aef",
                         "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/innerdistance": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3e839096a1be5da4f68d1de1066e4d0bc13f5d6d",
                         "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/junctionannotation": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
                         "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/junctionsaturation": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "9dfed3180f80f599c91daf5112d73a5e59367c24",
                         "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/readdistribution": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "7bb1b295a359bcbf0a0ea03d19d40a00916805ee",
                         "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/readduplication": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "db02573fdd89210d09ce9e2ac06857902a7fffec",
                         "installed_by": ["bam_rseqc"]
                     },
                     "rseqc/tin": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "4acfdd20843d5b6d63f9181721a6856447cb7bec",
                         "installed_by": ["bam_rseqc"]
                     },
                     "salmon/index": {
@@ -152,31 +152,31 @@
                     },
                     "samtools/flagstat": {
                         "branch": "master",
-                        "git_sha": "570ec5bcfe19c49e16c9ca35a7a116563af6cc1c",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/idxstats": {
                         "branch": "master",
-                        "git_sha": "e662ab16e0c11f1e62983e21de9871f59371a639",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": [
+                            "bam_dedup_stats_samtools_umitools",
                             "bam_markduplicates_picard",
-                            "bam_sort_stats_samtools",
-                            "bam_dedup_stats_samtools_umitools"
+                            "bam_sort_stats_samtools"
                         ]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_sort_stats_samtools"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "735e1e04e7e01751d2d6e97055bbdb6f70683cc1",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["bam_stats_samtools"]
                     },
                     "sortmerna": {
@@ -206,7 +206,7 @@
                     },
                     "trimgalore": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["fastq_fastqc_umitools_trimgalore"]
                     },
                     "ucsc/bedclip": {
@@ -221,13 +221,13 @@
                     },
                     "umitools/dedup": {
                         "branch": "master",
-                        "git_sha": "7297204bf49273300a3dbfa4b7a4027c8683f1bd",
+                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
                         "installed_by": ["bam_dedup_stats_samtools_umitools"]
                     },
                     "umitools/extract": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
-                        "installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
+                        "git_sha": "65ad3e0b9a4099592e1102e92e10455dc661cf53",
+                        "installed_by": ["fastq_fastqc_umitools_trimgalore", "fastq_fastqc_umitools_fastp"]
                     },
                     "untar": {
                         "branch": "master",
@@ -240,31 +240,31 @@
                 "nf-core": {
                     "bam_dedup_stats_samtools_umitools": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_markduplicates_picard": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_rseqc": {
                         "branch": "master",
-                        "git_sha": "a9784afdd5dcda23b84e64db75dc591065d64653",
+                        "git_sha": "92793c143c93acd9129f15f35f25d3aab2b23c0e",
                         "installed_by": ["subworkflows"]
                     },
                     "bam_sort_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["fastq_align_hisat2"]
                     },
                     "bam_stats_samtools": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": [
-                            "bam_sort_stats_samtools",
+                            "bam_dedup_stats_samtools_umitools",
                             "bam_markduplicates_picard",
-                            "bam_dedup_stats_samtools_umitools"
+                            "bam_sort_stats_samtools"
                         ]
                     },
                     "bedgraph_bedclip_bedgraphtobigwig": {
@@ -279,12 +279,12 @@
                     },
                     "fastq_fastqc_umitools_fastp": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "3e8b0c1144ccf60b7848efbdc2be285ff20b49ee",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_fastqc_umitools_trimgalore": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f",
                         "installed_by": ["subworkflows"]
                     },
                     "fastq_subsample_fq_salmon": {

diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml
diff --git a/modules/nf-core/fastp/main.nf b/modules/nf-core/fastp/main.nf
diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml