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Merge pull request #77 from fulaibaowang/nf-test-conda-env
nf-test-conda-env
2 parents 6de58a6 + ed89416 commit 91b0f8c

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‎modules/local/fraser/annotategenes/environment.yml‎

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@@ -19,3 +19,5 @@ dependencies:
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- conda-forge::r-rmarkdown=2.29
2020
- conda-forge::r-tidyr=1.3.1
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- conda-forge::r-yaml=2.3.10
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- conda-forge::r-cowplot=1.1.3
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- conda-forge::r-rcolorbrewer=1.1_3

‎modules/local/fraser/annotategenes/main.nf‎

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@@ -5,8 +5,8 @@ process FRASER_ANNOTATEGENES {
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// TODO discuss if this container should be split up, library loading should be done in the module script instead in that case
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3e/3e8560898529101d3e70df5dc164124740084c05a48ced2baf0128379825d04e/data' :
9-
'community.wave.seqera.io/library/bioconductor-bsgenome.hsapiens.ucsc.hg19_bioconductor-bsgenome.hsapiens.ucsc.hg38_bioconductor-bsgenome_bioconductor-delayedmatrixstats_pruned:6ecb1e6b5187b515' }"
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c87aab5452ff7d6a9344148e284ca01a8c5d2239d7b0f26164da1806a8c59875/data' :
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'community.wave.seqera.io/library/bioconductor-bsgenome.hsapiens.ucsc.hg19_bioconductor-bsgenome.hsapiens.ucsc.hg38_bioconductor-bsgenome_bioconductor-delayedmatrixstats_pruned:b2aa4004c588aaaf' }"
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input:
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tuple val(meta), path(fds, stageAs: "input/savedObjects/*"), path(txdb), path(gene_name_mapping), val(drop_group), val(annotation_id)

‎modules/local/fraser/calculatestats/environment.yml‎

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@@ -19,3 +19,5 @@ dependencies:
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- conda-forge::r-rmarkdown=2.29
2020
- conda-forge::r-tidyr=1.3.1
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- conda-forge::r-yaml=2.3.10
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- conda-forge::r-cowplot=1.1.3
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- conda-forge::r-rcolorbrewer=1.1_3

‎modules/local/fraser/calculatestats/main.nf‎

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@@ -5,8 +5,8 @@ process FRASER_CALCULATESTATS {
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// TODO discuss if this container should be split up, library loading should be done in the module script instead in that case
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3e/3e8560898529101d3e70df5dc164124740084c05a48ced2baf0128379825d04e/data' :
9-
'community.wave.seqera.io/library/bioconductor-bsgenome.hsapiens.ucsc.hg19_bioconductor-bsgenome.hsapiens.ucsc.hg38_bioconductor-bsgenome_bioconductor-delayedmatrixstats_pruned:6ecb1e6b5187b515' }"
8+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c87aab5452ff7d6a9344148e284ca01a8c5d2239d7b0f26164da1806a8c59875/data' :
9+
'community.wave.seqera.io/library/bioconductor-bsgenome.hsapiens.ucsc.hg19_bioconductor-bsgenome.hsapiens.ucsc.hg38_bioconductor-bsgenome_bioconductor-delayedmatrixstats_pruned:b2aa4004c588aaaf' }"
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input:
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tuple val(meta), path(fds, stageAs: "input/savedObjects/*"), val(drop_group), val(annotation_id), val(sample_ids)

‎modules/local/fraser/calculatestats/tests/main.nf.test‎

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@@ -50,8 +50,8 @@ nextflow_process {
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assertAll (
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{ assert process.success },
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{ assert snapshot(
53-
file_list.findAll { file(it.toString()).name != "fds-object.RDS"},
54-
file_list.findAll { file(it.toString()).name == "fds-object.RDS"}.collect { file(it.toString()).name },
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file_list.findAll { !(file(it.toString()).name in ["fds-object.RDS", "pvaluesBetaBinomial_psi5.h5", "pvaluesBetaBinomial_theta.h5", "pvaluesBetaBinomial_junction_psi5.h5", "pvaluesBetaBinomial_junction_theta.h5"])},
54+
file_list.findAll { file(it.toString()).name in ["fds-object.RDS", "pvaluesBetaBinomial_psi5.h5", "pvaluesBetaBinomial_theta.h5", "pvaluesBetaBinomial_junction_psi5.h5", "pvaluesBetaBinomial_junction_theta.h5"]}.collect { file(it.toString()).name },
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process.out.versions
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).match() }
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)

‎modules/local/fraser/calculatestats/tests/main.nf.test.snap‎

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@@ -22,11 +22,7 @@
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"psi3.h5:md5,e4718d51a2deba1a3eac0dd0ecfe725a",
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"psi5.h5:md5,bc4a333776535472090ad585e8e006ef",
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"pvaluesBetaBinomial_junction_psi3.h5:md5,2c40c6916d6a674ac797f7eb9af1f3e0",
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"pvaluesBetaBinomial_junction_psi5.h5:md5,bf4a9ea1d840bfda7133e3af9be12066",
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"pvaluesBetaBinomial_junction_theta.h5:md5,4df41aabd4e876d2c965916e515ad793",
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"pvaluesBetaBinomial_psi3.h5:md5,ce595a8ef6d382859108f9f23eb7cd58",
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"pvaluesBetaBinomial_psi5.h5:md5,0e176c189b747394b1a135a137fd81cd",
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"pvaluesBetaBinomial_theta.h5:md5,f09966dd529f5d54cb4c3be1d8190554",
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"rawCountsJ.h5:md5,64f8b27cc8cb2bc47de81f0a8cdf51e5",
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"rawCountsJnonsplit.h5:md5,769e925164bf81231c9b325954171e6a",
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"rawCountsSS.h5:md5,1bd7d5c2256f1c509142d8a779929f01",
@@ -37,7 +33,11 @@
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"theta.h5:md5,45e4ee34c95792a5b15f566fcadeee21"
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],
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[
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"fds-object.RDS"
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"fds-object.RDS",
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"pvaluesBetaBinomial_junction_psi5.h5",
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"pvaluesBetaBinomial_junction_theta.h5",
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"pvaluesBetaBinomial_psi5.h5",
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"pvaluesBetaBinomial_theta.h5"
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],
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[
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"versions.yml:md5,c2230506da2802610cc2143196972faf"
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"nf-test": "0.9.2",
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"nextflow": "25.04.6"
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},
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"timestamp": "2025-08-12T13:33:08.458817805"
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"timestamp": "2025-09-09T12:24:11.592076778"
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},
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"homo_sapiens - fds, cache - stub": {
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"content": [

‎modules/local/fraser/extractresults/environment.yml‎

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@@ -19,3 +19,5 @@ dependencies:
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- conda-forge::r-rmarkdown=2.29
2020
- conda-forge::r-tidyr=1.3.1
2121
- conda-forge::r-yaml=2.3.10
22+
- conda-forge::r-cowplot=1.1.3
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- conda-forge::r-rcolorbrewer=1.1_3

‎modules/local/fraser/extractresults/main.nf‎

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@@ -5,8 +5,8 @@ process FRASER_EXTRACTRESULTS {
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// TODO discuss if this container should be split up, library loading should be done in the module script instead in that case
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3e/3e8560898529101d3e70df5dc164124740084c05a48ced2baf0128379825d04e/data' :
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'community.wave.seqera.io/library/bioconductor-bsgenome.hsapiens.ucsc.hg19_bioconductor-bsgenome.hsapiens.ucsc.hg38_bioconductor-bsgenome_bioconductor-delayedmatrixstats_pruned:6ecb1e6b5187b515' }"
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c87aab5452ff7d6a9344148e284ca01a8c5d2239d7b0f26164da1806a8c59875/data' :
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'community.wave.seqera.io/library/bioconductor-bsgenome.hsapiens.ucsc.hg19_bioconductor-bsgenome.hsapiens.ucsc.hg38_bioconductor-bsgenome_bioconductor-delayedmatrixstats_pruned:b2aa4004c588aaaf' }"
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input:
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tuple val(meta), path(fds, stageAs: 'input/savedObjects/*'), path(txdb), val(drop_group), val(annotation_id), val(sample_ids)

‎modules/local/fraser/filterexpression/environment.yml‎

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@@ -19,3 +19,5 @@ dependencies:
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- conda-forge::r-rmarkdown=2.29
2020
- conda-forge::r-tidyr=1.3.1
2121
- conda-forge::r-yaml=2.3.10
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- conda-forge::r-cowplot=1.1.3
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- conda-forge::r-rcolorbrewer=1.1_3

‎modules/local/fraser/filterexpression/main.nf‎

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@@ -5,8 +5,8 @@ process FRASER_FILTEREXPRESSION {
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// TODO discuss if this container should be split up, library loading should be done in the module script instead in that case
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conda "${moduleDir}/environment.yml"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3e/3e8560898529101d3e70df5dc164124740084c05a48ced2baf0128379825d04e/data' :
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'community.wave.seqera.io/library/bioconductor-bsgenome.hsapiens.ucsc.hg19_bioconductor-bsgenome.hsapiens.ucsc.hg38_bioconductor-bsgenome_bioconductor-delayedmatrixstats_pruned:6ecb1e6b5187b515' }"
8+
'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/c8/c87aab5452ff7d6a9344148e284ca01a8c5d2239d7b0f26164da1806a8c59875/data' :
9+
'community.wave.seqera.io/library/bioconductor-bsgenome.hsapiens.ucsc.hg19_bioconductor-bsgenome.hsapiens.ucsc.hg38_bioconductor-bsgenome_bioconductor-delayedmatrixstats_pruned:b2aa4004c588aaaf' }"
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input:
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tuple val(meta), path(fds, stageAs: "input/savedObjects/*"), path(splice_counts_dirs), val(external_count_ids), val(drop_group)

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