From 7e6827e420585f59edf1e22c02b440f51c8eec61 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 20 Jun 2024 12:32:33 +0100 Subject: [PATCH 1/2] Move Conda dependencies for local modules to individual environment file --- modules/local/deseq2_qc/environment.yml | 15 +++++++++++++++ modules/local/deseq2_qc/main.nf | 2 +- modules/local/gtf2bed/environment.yml | 7 +++++++ modules/local/gtf2bed/main.nf | 2 +- modules/local/gtf_filter/environment.yml | 7 +++++++ modules/local/gtf_filter/main.nf | 2 +- .../local/multiqc_custom_biotype/environment.yml | 7 +++++++ modules/local/multiqc_custom_biotype/main.nf | 2 +- .../environment.yml | 7 +++++++ .../preprocess_transcripts_fasta_gencode/main.nf | 2 +- modules/local/rsem_merge_counts/environment.yml | 7 +++++++ modules/local/rsem_merge_counts/main.nf | 2 +- modules/local/star_align_igenomes/environment.yml | 9 +++++++++ modules/local/star_align_igenomes/main.nf | 2 +- .../local/star_align_igenomes/tests/main.nf.test | 1 - .../star_genomegenerate_igenomes/environment.yml | 9 +++++++++ .../local/star_genomegenerate_igenomes/main.nf | 2 +- 17 files changed, 76 insertions(+), 9 deletions(-) create mode 100644 modules/local/deseq2_qc/environment.yml create mode 100644 modules/local/gtf2bed/environment.yml create mode 100644 modules/local/gtf_filter/environment.yml create mode 100644 modules/local/multiqc_custom_biotype/environment.yml create mode 100644 modules/local/preprocess_transcripts_fasta_gencode/environment.yml create mode 100644 modules/local/rsem_merge_counts/environment.yml create mode 100644 modules/local/star_align_igenomes/environment.yml create mode 100644 modules/local/star_genomegenerate_igenomes/environment.yml diff --git a/modules/local/deseq2_qc/environment.yml b/modules/local/deseq2_qc/environment.yml new file mode 100644 index 000000000..9daad310d --- /dev/null +++ b/modules/local/deseq2_qc/environment.yml @@ -0,0 +1,15 @@ +name: deseq2_qc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::r-base + - conda-forge::r-optparse + - conda-forge::r-ggplot2 + - conda-forge::r-rcolorbrewer + - conda-forge::r-pheatmap + - bioconda::bioconductor-deseq2 + - bioconda::bioconductor-biocparallel + - bioconda::bioconductor-tximport + - bioconda::bioconductor-complexheatmap diff --git a/modules/local/deseq2_qc/main.nf b/modules/local/deseq2_qc/main.nf index 466194934..7be6836f6 100644 --- a/modules/local/deseq2_qc/main.nf +++ b/modules/local/deseq2_qc/main.nf @@ -3,7 +3,7 @@ process DESEQ2_QC { // (Bio)conda packages have intentionally not been pinned to a specific version // This was to avoid the pipeline failing due to package conflicts whilst creating the environment when using -profile conda - conda "conda-forge::r-base bioconda::bioconductor-deseq2 bioconda::bioconductor-biocparallel bioconda::bioconductor-tximport bioconda::bioconductor-complexheatmap conda-forge::r-optparse conda-forge::r-ggplot2 conda-forge::r-rcolorbrewer conda-forge::r-pheatmap" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' : 'biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0' }" diff --git a/modules/local/gtf2bed/environment.yml b/modules/local/gtf2bed/environment.yml new file mode 100644 index 000000000..3c009b31b --- /dev/null +++ b/modules/local/gtf2bed/environment.yml @@ -0,0 +1,7 @@ +name: gtf2bed +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::perl=5.26.2 diff --git a/modules/local/gtf2bed/main.nf b/modules/local/gtf2bed/main.nf index 8a4bae8ff..464d7f819 100644 --- a/modules/local/gtf2bed/main.nf +++ b/modules/local/gtf2bed/main.nf @@ -2,7 +2,7 @@ process GTF2BED { tag "$gtf" label 'process_low' - conda "conda-forge::perl=5.26.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/perl:5.26.2' : 'biocontainers/perl:5.26.2' }" diff --git a/modules/local/gtf_filter/environment.yml b/modules/local/gtf_filter/environment.yml new file mode 100644 index 000000000..c8b5ca202 --- /dev/null +++ b/modules/local/gtf_filter/environment.yml @@ -0,0 +1,7 @@ +name: gtf_filter +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::python=3.9.5 diff --git a/modules/local/gtf_filter/main.nf b/modules/local/gtf_filter/main.nf index d14e8ff42..39b215712 100644 --- a/modules/local/gtf_filter/main.nf +++ b/modules/local/gtf_filter/main.nf @@ -1,7 +1,7 @@ process GTF_FILTER { tag "$fasta" - conda "conda-forge::python=3.9.5" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.9--1' : 'biocontainers/python:3.9--1' }" diff --git a/modules/local/multiqc_custom_biotype/environment.yml b/modules/local/multiqc_custom_biotype/environment.yml new file mode 100644 index 000000000..7a6b5722e --- /dev/null +++ b/modules/local/multiqc_custom_biotype/environment.yml @@ -0,0 +1,7 @@ +name: multiqc_custom_biotype +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::python=3.9.5 diff --git a/modules/local/multiqc_custom_biotype/main.nf b/modules/local/multiqc_custom_biotype/main.nf index 9c0fe94eb..d102f67d9 100644 --- a/modules/local/multiqc_custom_biotype/main.nf +++ b/modules/local/multiqc_custom_biotype/main.nf @@ -1,7 +1,7 @@ process MULTIQC_CUSTOM_BIOTYPE { tag "$meta.id" - conda "conda-forge::python=3.9.5" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/python:3.9--1' : 'biocontainers/python:3.9--1' }" diff --git a/modules/local/preprocess_transcripts_fasta_gencode/environment.yml b/modules/local/preprocess_transcripts_fasta_gencode/environment.yml new file mode 100644 index 000000000..06e4d9658 --- /dev/null +++ b/modules/local/preprocess_transcripts_fasta_gencode/environment.yml @@ -0,0 +1,7 @@ +name: preprocess_transcripts_fasta_gencode +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 diff --git a/modules/local/preprocess_transcripts_fasta_gencode/main.nf b/modules/local/preprocess_transcripts_fasta_gencode/main.nf index 41f1d42f6..9d530b77d 100644 --- a/modules/local/preprocess_transcripts_fasta_gencode/main.nf +++ b/modules/local/preprocess_transcripts_fasta_gencode/main.nf @@ -1,7 +1,7 @@ process PREPROCESS_TRANSCRIPTS_FASTA_GENCODE { tag "$fasta" - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/local/rsem_merge_counts/environment.yml b/modules/local/rsem_merge_counts/environment.yml new file mode 100644 index 000000000..eeeb3329a --- /dev/null +++ b/modules/local/rsem_merge_counts/environment.yml @@ -0,0 +1,7 @@ +name: rsem_merge_counts +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - conda-forge::sed=4.7 diff --git a/modules/local/rsem_merge_counts/main.nf b/modules/local/rsem_merge_counts/main.nf index 3f226f54d..b21ca4aa4 100644 --- a/modules/local/rsem_merge_counts/main.nf +++ b/modules/local/rsem_merge_counts/main.nf @@ -1,7 +1,7 @@ process RSEM_MERGE_COUNTS { label "process_medium" - conda "conda-forge::sed=4.7" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : 'nf-core/ubuntu:20.04' }" diff --git a/modules/local/star_align_igenomes/environment.yml b/modules/local/star_align_igenomes/environment.yml new file mode 100644 index 000000000..0d92f8dd5 --- /dev/null +++ b/modules/local/star_align_igenomes/environment.yml @@ -0,0 +1,9 @@ +name: star_align_igenomes +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::star=2.6.1d + - bioconda::samtools=1.10 + - conda-forge::gawk=5.1.0 diff --git a/modules/local/star_align_igenomes/main.nf b/modules/local/star_align_igenomes/main.nf index 32f3cac29..04068f142 100644 --- a/modules/local/star_align_igenomes/main.nf +++ b/modules/local/star_align_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_ALIGN_IGENOMES { tag "$meta.id" label 'process_high' - conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" diff --git a/modules/local/star_align_igenomes/tests/main.nf.test b/modules/local/star_align_igenomes/tests/main.nf.test index 088796410..91be69f01 100644 --- a/modules/local/star_align_igenomes/tests/main.nf.test +++ b/modules/local/star_align_igenomes/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process STAR_ALIGN_IGENOMES" script "../main.nf" process "STAR_ALIGN_IGENOMES" - tag "STAR_ALIGN_IGENOMES" tag "STAR_GENOMEGENERATE_IGENOMES" setup { diff --git a/modules/local/star_genomegenerate_igenomes/environment.yml b/modules/local/star_genomegenerate_igenomes/environment.yml new file mode 100644 index 000000000..c3c6c2481 --- /dev/null +++ b/modules/local/star_genomegenerate_igenomes/environment.yml @@ -0,0 +1,9 @@ +name: star_genomegenerate_igenomes +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::star=2.6.1d + - bioconda::samtools=1.10 + - conda-forge::gawk=5.1.0 diff --git a/modules/local/star_genomegenerate_igenomes/main.nf b/modules/local/star_genomegenerate_igenomes/main.nf index 814bc7c8c..7b5115a6c 100644 --- a/modules/local/star_genomegenerate_igenomes/main.nf +++ b/modules/local/star_genomegenerate_igenomes/main.nf @@ -2,7 +2,7 @@ process STAR_GENOMEGENERATE_IGENOMES { tag "$fasta" label 'process_high' - conda "bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' : 'biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0' }" From 928a30ef714a3d073ede26943d69b347c65b3bd2 Mon Sep 17 00:00:00 2001 From: Harshil Patel Date: Thu, 20 Jun 2024 12:34:05 +0100 Subject: [PATCH 2/2] Update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f8f5b273..651d6fe8c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -79,6 +79,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1312](https://github.com/nf-core/rnaseq/pull/1312) - Fix issues with unzipping of GTF/ GFF files without absolute paths - [PR #1322](https://github.com/nf-core/rnaseq/pull/1322) - Use pre-built Github Action to detect nf-test changes - [PR #1306](https://github.com/nf-core/rnaseq/pull/1306) - Overhaul strandedness detection / comparison +- [PR #1326](https://github.com/nf-core/rnaseq/pull/1326) - Move Conda dependencies for local modules to individual environment file ### Parameters