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Merge pull request #1335 from maxulysse/stubs_everywhere
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Adding stubs at all level
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@maxulysse
maxulysse committed Aug 21, 2024
2 parents 75995bf + 1b34d1e commit ad43736
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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
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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- [PR #1340](https://github.com/nf-core/rnaseq/pull/1340) - Remove out-of-date Azure specific guidance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.
>
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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": {
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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 $counts -n 1 | cut -f3-`;
do
touch size_factors/\${i}.size_factors.RData
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4 changes: 2 additions & 2 deletions modules/local/star_align_igenomes/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,8 @@ process STAR_ALIGN_IGENOMES {
stub:
def prefix = task.ext.prefix ?: "${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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