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Adding stubs at all level #1335

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merged 42 commits into from
Aug 21, 2024
Merged

Adding stubs at all level #1335

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0620d21
stub for align_star + a single snapshot match per test
maxulysse Jul 3, 2024
573ca90
add stubs + code polish + Harshil align
maxulysse Jul 3, 2024
3efcb84
add stub
maxulysse Jul 3, 2024
345d1f8
update all nf-core modules and subworkflows and do not include tags
maxulysse Jul 3, 2024
eb08f2f
simplify snapshot for stub
maxulysse Jul 3, 2024
c956f6f
add stubs for subworkflow local quantify_rsem
maxulysse Jul 3, 2024
bf5797f
update default snapshot
maxulysse Jul 3, 2024
37780ad
add plugin
maxulysse Jul 4, 2024
150ac0b
update all subworkflows
maxulysse Jul 4, 2024
9fd07da
do not snapshot fastq in stub
maxulysse Jul 4, 2024
2cdeea1
pipeline level stub
maxulysse Jul 4, 2024
3c78a6a
fix stub test for prepare_genome
maxulysse Jul 4, 2024
c572fc0
update all subworkflows
maxulysse Jul 4, 2024
df9efba
correctly align
maxulysse Jul 5, 2024
bc7d7a5
update all modules
maxulysse Jul 9, 2024
b78a653
use seqera containers
maxulysse Jul 11, 2024
98cf1fa
Merge branch 'dev' into stubs_everywhere
maxulysse Jul 12, 2024
8759ed7
update all modules/subworkflows + remove tags
maxulysse Jul 12, 2024
5c1db07
update snapshot
maxulysse Jul 12, 2024
3c9250d
Merge branch 'dev' into stubs_everywhere
maxulysse Jul 16, 2024
8052b6b
Merge branch 'dev' into stubs_everywhere
maxulysse Jul 22, 2024
8b28fee
update nf-test to 0.9.0
maxulysse Jul 22, 2024
3eaf7a4
sort
maxulysse Jul 22, 2024
86bac63
update all modules/subworkflows + remove tags
maxulysse Jul 22, 2024
ee285c8
remove tags
maxulysse Jul 22, 2024
88286cd
keep card 3.1.1 that does not break CI due to weird RG
maxulysse Jul 22, 2024
f5adb7a
update snapshot
maxulysse Jul 22, 2024
d1c19be
update snapshot
maxulysse Jul 22, 2024
f94beb3
update all modules + subworkflows / remove tags + path markduplicates
maxulysse Jul 22, 2024
784aeb2
update snapshots
maxulysse Jul 22, 2024
30afc0e
update stringtie_stringtie
maxulysse Jul 22, 2024
58cee58
update snapshots for fastq_align_hisat2
maxulysse Jul 22, 2024
586058b
add proper stubs and tests for local star_*_igenomes modules
maxulysse Jul 22, 2024
32a6440
Merge branch 'dev' into stubs_everywhere
maxulysse Aug 16, 2024
f77e714
proper sha for module bedtools/genomecov
maxulysse Aug 16, 2024
200d4bd
update samtools/stats module + rm tags
maxulysse Aug 16, 2024
34fecc9
Merge branch 'dev' into stubs_everywhere
maxulysse Aug 20, 2024
3088bde
clean up stub tests
maxulysse Aug 20, 2024
a0499c8
Merge branch 'dev' into stubs_everywhere
maxulysse Aug 20, 2024
56539ac
update CHANGELOG
maxulysse Aug 20, 2024
a68cb69
update snapshot
maxulysse Aug 20, 2024
1b34d1e
update snapshot
maxulysse Aug 21, 2024
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ on:

env:
NXF_ANSI_LOG: false
NFT_VER: "0.8.4"
NFT_VER: "0.9.0"
NFT_WORKDIR: "~"
NFT_DIFF: "pdiff"
NFT_DIFF_ARGS: "--line-numbers --expand-tabs=2"
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -102,6 +102,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
- [PR #1330](https://github.com/nf-core/rnaseq/pull/1330) - Update all nf-core/modules and subworkflows
- [PR #1331](https://github.com/nf-core/rnaseq/pull/1331) - Adding stubs for local modules
- [PR #1334](https://github.com/nf-core/rnaseq/pull/1334) - Update all nf-core/modules and subworkflows with stubs
- [PR #1335](https://github.com/nf-core/rnaseq/pull/1335) - Adding stubs at all levels
- [PR #1336](https://github.com/nf-core/rnaseq/pull/1334) - Use nf-core/setup-nf-test to install nf-test from cache during CI/CD
- [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance
- [PR #1341](https://github.com/nf-core/rnaseq/pull/1341) - Add rename in the MultiQC report for samples without techreps
Expand Down Expand Up @@ -137,6 +138,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements
| `samtools` | 1.17 | 1.20 |
| `sortmerna` | 4.3.4 | 4.3.6 |
| `umi_tools` | 1.14 | 1.15 |
| `untar` | 1.3 | 1.34 |

> **NB:** Dependency has been **updated** if both old and new version information is present.
>
Expand Down
73 changes: 37 additions & 36 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@
"nf-core": {
"bbmap/bbsplit": {
"branch": "master",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
},
"bedtools/genomecov": {
Expand All @@ -17,22 +17,22 @@
},
"cat/fastq": {
"branch": "master",
"git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e",
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "modules"]
},
"custom/catadditionalfasta": {
"branch": "master",
"git_sha": "2c6b1144ed58b6184ad58fc4e6b6a90219b4bf4f",
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
"installed_by": ["modules"]
},
"custom/getchromsizes": {
"branch": "master",
"git_sha": "41a4135c502b42ede663af87efa70a96ecbd7cb9",
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
"installed_by": ["modules"]
},
"custom/tx2gene": {
"branch": "master",
"git_sha": "82024cf6325d2ee194e7f056d841ecad2f6856e9",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"installed_by": ["modules", "quantify_pseudo_alignment"]
},
"dupradar": {
Expand All @@ -42,12 +42,12 @@
},
"fastp": {
"branch": "master",
"git_sha": "b90b5cd93149a1b3be263d916c7234fe0708a71c",
"git_sha": "1ceaa8ba4d0fd886dbca0e545815d905b7407de7",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"fastqc": {
"branch": "master",
"git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["fastq_fastqc_umitools_fastp", "fastq_fastqc_umitools_trimgalore"]
},
"fq/subsample": {
Expand All @@ -62,7 +62,7 @@
},
"gunzip": {
"branch": "master",
"git_sha": "a7231cbccb86535529e33859e05d19ac93f3ea04",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"installed_by": ["modules"]
},
"hisat2/align": {
Expand All @@ -82,12 +82,12 @@
},
"kallisto/index": {
"branch": "master",
"git_sha": "de5811dd9ca15af1e131806001bcaae909e42021",
"git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
"installed_by": ["modules"]
},
"kallisto/quant": {
"branch": "master",
"git_sha": "de5811dd9ca15af1e131806001bcaae909e42021",
"git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
"installed_by": ["modules", "quantify_pseudo_alignment"]
},
"multiqc": {
Expand All @@ -97,8 +97,9 @@
},
"picard/markduplicates": {
"branch": "master",
"git_sha": "1943aa60f7490c3d6740e8872e6e69122ccc8087",
"installed_by": ["bam_markduplicates_picard"]
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_markduplicates_picard"],
"patch": "modules/nf-core/picard/markduplicates/picard-markduplicates.diff"
},
"preseq/lcextrap": {
"branch": "master",
Expand All @@ -107,7 +108,7 @@
},
"qualimap/rnaseq": {
"branch": "master",
"git_sha": "6b0e4fe14ca1b12e131f64608f0bbaf36fd11451",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["modules"]
},
"rsem/calculateexpression": {
Expand Down Expand Up @@ -172,17 +173,17 @@
},
"samtools/flagstat": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_stats_samtools"]
},
"samtools/idxstats": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_stats_samtools"]
},
"samtools/index": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": [
"bam_dedup_stats_samtools_umitools",
"bam_markduplicates_picard",
Expand All @@ -191,12 +192,12 @@
},
"samtools/sort": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bam_sort_stats_samtools"]
},
"samtools/stats": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "1fe379cf6e6c1e6fa5e32bcbeefea0f1e874dac6",
"installed_by": ["bam_stats_samtools"]
},
"sortmerna": {
Expand All @@ -206,17 +207,17 @@
},
"star/align": {
"branch": "master",
"git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["modules"]
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "a21faa6a3481af92a343a10926f59c189a2c16c9",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["modules"]
},
"stringtie/stringtie": {
"branch": "master",
"git_sha": "b1b959609bda44341120aed1766329909f54b8d0",
"git_sha": "c789476080a150f87066ca3ed42a622339a26c0b",
"installed_by": ["modules"]
},
"subread/featurecounts": {
Expand All @@ -226,7 +227,7 @@
},
"summarizedexperiment/summarizedexperiment": {
"branch": "master",
"git_sha": "31751460f9ce9552846e13fdeec6953dcb47132d",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"installed_by": ["modules", "quantify_pseudo_alignment"]
},
"trimgalore": {
Expand All @@ -246,12 +247,12 @@
},
"ucsc/bedgraphtobigwig": {
"branch": "master",
"git_sha": "7c75d01997236f61b9b77399d9933cb36041f2c3",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["bedgraph_bedclip_bedgraphtobigwig"]
},
"umitools/dedup": {
"branch": "master",
"git_sha": "3bd4f34e3093c2a16e6a8eefc22242b9b94641db",
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
"installed_by": ["bam_dedup_stats_samtools_umitools"]
},
"umitools/extract": {
Expand All @@ -266,7 +267,7 @@
},
"untar": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d",
"installed_by": ["modules"]
}
}
Expand All @@ -275,27 +276,27 @@
"nf-core": {
"bam_dedup_stats_samtools_umitools": {
"branch": "master",
"git_sha": "8f2062e7b4185590fb9f43c275381a31a6544fc0",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["subworkflows"]
},
"bam_markduplicates_picard": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["subworkflows"]
},
"bam_rseqc": {
"branch": "master",
"git_sha": "9eb22e4d3f28c274b7c498a1564581377349a242",
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
"installed_by": ["subworkflows"]
},
"bam_sort_stats_samtools": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["fastq_align_hisat2"]
},
"bam_stats_samtools": {
"branch": "master",
"git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
"installed_by": [
"bam_dedup_stats_samtools_umitools",
"bam_markduplicates_picard",
Expand All @@ -304,22 +305,22 @@
},
"bedgraph_bedclip_bedgraphtobigwig": {
"branch": "master",
"git_sha": "a4bceac1aecee5aa0a5dbc601baf0e2e61013fb2",
"git_sha": "0eacd714effe5aac1c1de26593873960b3346cab",
"installed_by": ["subworkflows"]
},
"fastq_align_hisat2": {
"branch": "master",
"git_sha": "c60c14b285b89bdd0607e371417dadb80385ad6e",
"git_sha": "c789476080a150f87066ca3ed42a622339a26c0b",
"installed_by": ["subworkflows"]
},
"fastq_fastqc_umitools_fastp": {
"branch": "master",
"git_sha": "db35d26edeafacf9906a517827df621a29adc13d",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
},
"fastq_fastqc_umitools_trimgalore": {
"branch": "master",
"git_sha": "cb6defa0834eda9d6d3f967e981c819fc3e257bf",
"git_sha": "46eca555142d6e597729fcb682adcc791796f514",
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
},
"fastq_qc_trim_filter_setstrandedness": {
Expand All @@ -329,12 +330,12 @@
},
"fastq_subsample_fq_salmon": {
"branch": "master",
"git_sha": "727232afb8294b53dd9d05bfe469b70cce1675bb",
"git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
"installed_by": ["fastq_qc_trim_filter_setstrandedness", "subworkflows"]
},
"quantify_pseudo_alignment": {
"branch": "master",
"git_sha": "5d095e8413da1f4c72b7d07ce87f75c09482486f",
"git_sha": "fbe341e9af0bb98533757f536b26d38507d31724",
"installed_by": ["subworkflows"]
},
"utils_nextflow_pipeline": {
Expand Down
6 changes: 3 additions & 3 deletions modules/local/deseq2_qc/main.nf
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Expand Up @@ -63,16 +63,16 @@ process DESEQ2_QC {
def label_lower = args2.toLowerCase()
prefix = task.ext.prefix ?: "deseq2"
"""
mkdir size_factors
touch ${label_lower}.pca.vals_mqc.tsv
touch ${label_lower}.sample.dists_mqc.tsv
touch ${prefix}.plots.pdf
touch ${prefix}.dds.RData
touch ${prefix}.pca.vals.txt
touch ${prefix}.plots.pdf
touch ${prefix}.sample.dists.txt
touch R_sessionInfo.log
touch size_factors/${prefix}.size_factors.RData

mkdir size_factors
touch size_factors/${prefix}.size_factors.RData
for i in `head $counts -n 1 | cut -f3-`;
do
touch size_factors/\${i}.size_factors.RData
Expand Down
4 changes: 2 additions & 2 deletions modules/local/star_align_igenomes/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,8 @@ process STAR_ALIGN_IGENOMES {
stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
echo "" | gzip > ${prefix}.unmapped_1.fastq.gz
echo "" | gzip > ${prefix}.unmapped_2.fastq.gz
touch ${prefix}Xd.out.bam
touch ${prefix}.Log.final.out
touch ${prefix}.Log.out
Expand All @@ -84,8 +86,6 @@ process STAR_ALIGN_IGENOMES {
touch ${prefix}.toTranscriptome.out.bam
touch ${prefix}.Aligned.unsort.out.bam
touch ${prefix}.Aligned.sortedByCoord.out.bam
touch ${prefix}.unmapped_1.fastq.gz
touch ${prefix}.unmapped_2.fastq.gz
touch ${prefix}.tab
touch ${prefix}.SJ.out.tab
touch ${prefix}.ReadsPerGene.out.tab
Expand Down
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