From d9949cf008fdf56e48d79b221d582cfeb699e209 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 10 Sep 2024 13:51:51 +0200 Subject: [PATCH 1/4] replace gatk4 container --- modules.json | 189 +++++++++++++----- .../gatk4-calibratedragstrmodel.diff | 21 ++ .../gatk4/calibratedragstrmodel/main.nf | 4 +- .../gatk4-composestrtablefile.diff | 21 ++ .../nf-core/gatk4/composestrtablefile/main.nf | 4 +- .../gatk4-createsequencedictionary.diff | 22 ++ .../gatk4/createsequencedictionary/main.nf | 4 +- .../gatk4-genomicsdbimport.diff | 23 +++ .../nf-core/gatk4/genomicsdbimport/main.nf | 4 +- .../genotypegvcfs/gatk4-genotypegvcfs.diff | 21 ++ modules/nf-core/gatk4/genotypegvcfs/main.nf | 4 +- .../gatk4-haplotypecaller.diff | 22 ++ modules/nf-core/gatk4/haplotypecaller/main.nf | 4 +- 13 files changed, 285 insertions(+), 58 deletions(-) create mode 100644 modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff create mode 100644 modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff create mode 100644 modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff create mode 100644 modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff create mode 100644 modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff create mode 100644 modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff diff --git a/modules.json b/modules.json index 9693296c..628b4ea9 100644 --- a/modules.json +++ b/modules.json @@ -8,210 +8,299 @@ "bcftools/annotate": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "bcftools/filter": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/norm": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "bcftools/query": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/reheader": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bcftools/sort": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "bcftools/stats": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/intersect": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/merge": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "bedtools/split": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/download": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "ensemblvep/vep": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "gatk4/calibratedragstrmodel": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff" }, "gatk4/composestrtablefile": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff" }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff" }, "gatk4/genomicsdbimport": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff" }, "gatk4/genotypegvcfs": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff" }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff" }, "gawk": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mosdepth": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/format": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/pedfilter": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" }, "rtgtools/rocplot": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/convert": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/faidx": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "samtools/merge": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "snpeff/snpeff": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "vcf_annotate_ensemblvep_snpeff" + ] }, "somalier/extract": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "somalier/relate": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "tabix/bgzip": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "tabix/tabix": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"] + "installed_by": [ + "modules", + "vcf_annotate_ensemblvep_snpeff" + ] }, "untar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vardictjava": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcf2db": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "vcfanno": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] } } }, @@ -220,25 +309,33 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "vcf_annotate_ensemblvep_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff b/modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff new file mode 100644 index 00000000..cc4bba8c --- /dev/null +++ b/modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff @@ -0,0 +1,21 @@ +Changes in module 'nf-core/gatk4/calibratedragstrmodel' +'modules/nf-core/gatk4/calibratedragstrmodel/environment.yml' is unchanged +'modules/nf-core/gatk4/calibratedragstrmodel/meta.yml' is unchanged +Changes in 'gatk4/calibratedragstrmodel/main.nf': +--- modules/nf-core/gatk4/calibratedragstrmodel/main.nf ++++ modules/nf-core/gatk4/calibratedragstrmodel/main.nf +@@ -4,8 +4,8 @@ + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': +- 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" ++ 'broadinstitute/gatk:4.6.0.0': ++ 'broadinstitute/gatk:4.6.0.0' }" + + input: + tuple val(meta), path(bam), path(bam_index) + +'modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test.snap' is unchanged +'modules/nf-core/gatk4/calibratedragstrmodel/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index 88e108cb..a09822be 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'broadinstitute/gatk:4.6.0.0': + 'broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(bam), path(bam_index) diff --git a/modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff b/modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff new file mode 100644 index 00000000..b4b4d95d --- /dev/null +++ b/modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff @@ -0,0 +1,21 @@ +Changes in module 'nf-core/gatk4/composestrtablefile' +'modules/nf-core/gatk4/composestrtablefile/environment.yml' is unchanged +'modules/nf-core/gatk4/composestrtablefile/meta.yml' is unchanged +Changes in 'gatk4/composestrtablefile/main.nf': +--- modules/nf-core/gatk4/composestrtablefile/main.nf ++++ modules/nf-core/gatk4/composestrtablefile/main.nf +@@ -4,8 +4,8 @@ + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': +- 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" ++ 'broadinstitute/gatk:4.6.0.0': ++ 'broadinstitute/gatk:4.6.0.0' }" + + input: + path(fasta) + +'modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test.snap' is unchanged +'modules/nf-core/gatk4/composestrtablefile/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 5073ab64..2abda035 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -4,8 +4,8 @@ process GATK4_COMPOSESTRTABLEFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'broadinstitute/gatk:4.6.0.0': + 'broadinstitute/gatk:4.6.0.0' }" input: path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff b/modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff new file mode 100644 index 00000000..ea62947f --- /dev/null +++ b/modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff @@ -0,0 +1,22 @@ +Changes in module 'nf-core/gatk4/createsequencedictionary' +'modules/nf-core/gatk4/createsequencedictionary/environment.yml' is unchanged +'modules/nf-core/gatk4/createsequencedictionary/meta.yml' is unchanged +Changes in 'gatk4/createsequencedictionary/main.nf': +--- modules/nf-core/gatk4/createsequencedictionary/main.nf ++++ modules/nf-core/gatk4/createsequencedictionary/main.nf +@@ -4,8 +4,8 @@ + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': +- 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" ++ 'broadinstitute/gatk:4.6.0.0': ++ 'broadinstitute/gatk:4.6.0.0' }" + + input: + tuple val(meta), path(fasta) + +'modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test.snap' is unchanged +'modules/nf-core/gatk4/createsequencedictionary/tests/tags.yml' is unchanged +'modules/nf-core/gatk4/createsequencedictionary/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index c7f1d75b..d03f98af 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESEQUENCEDICTIONARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'broadinstitute/gatk:4.6.0.0': + 'broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff b/modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff new file mode 100644 index 00000000..2a94ac80 --- /dev/null +++ b/modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff @@ -0,0 +1,23 @@ +Changes in module 'nf-core/gatk4/genomicsdbimport' +'modules/nf-core/gatk4/genomicsdbimport/environment.yml' is unchanged +'modules/nf-core/gatk4/genomicsdbimport/meta.yml' is unchanged +Changes in 'gatk4/genomicsdbimport/main.nf': +--- modules/nf-core/gatk4/genomicsdbimport/main.nf ++++ modules/nf-core/gatk4/genomicsdbimport/main.nf +@@ -4,8 +4,8 @@ + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': +- 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" ++ 'broadinstitute/gatk:4.6.0.0': ++ 'broadinstitute/gatk:4.6.0.0' }" + + input: + tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) + +'modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test.snap' is unchanged +'modules/nf-core/gatk4/genomicsdbimport/tests/tags.yml' is unchanged +'modules/nf-core/gatk4/genomicsdbimport/tests/nextflow.config' is unchanged +'modules/nf-core/gatk4/genomicsdbimport/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 6f1d4c53..9c397744 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOMICSDBIMPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'broadinstitute/gatk:4.6.0.0': + 'broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff b/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff new file mode 100644 index 00000000..26e008be --- /dev/null +++ b/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff @@ -0,0 +1,21 @@ +Changes in module 'nf-core/gatk4/genotypegvcfs' +'modules/nf-core/gatk4/genotypegvcfs/environment.yml' is unchanged +'modules/nf-core/gatk4/genotypegvcfs/meta.yml' is unchanged +Changes in 'gatk4/genotypegvcfs/main.nf': +--- modules/nf-core/gatk4/genotypegvcfs/main.nf ++++ modules/nf-core/gatk4/genotypegvcfs/main.nf +@@ -4,8 +4,8 @@ + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': +- 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" ++ 'broadinstitute/gatk:4.6.0.0': ++ 'broadinstitute/gatk:4.6.0.0' }" + + input: + tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) + +'modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test.snap' is unchanged +'modules/nf-core/gatk4/genotypegvcfs/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index f180f749..fe6e0d0d 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOTYPEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'broadinstitute/gatk:4.6.0.0': + 'broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff b/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff new file mode 100644 index 00000000..f284375a --- /dev/null +++ b/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff @@ -0,0 +1,22 @@ +Changes in module 'nf-core/gatk4/haplotypecaller' +'modules/nf-core/gatk4/haplotypecaller/environment.yml' is unchanged +'modules/nf-core/gatk4/haplotypecaller/meta.yml' is unchanged +Changes in 'gatk4/haplotypecaller/main.nf': +--- modules/nf-core/gatk4/haplotypecaller/main.nf ++++ modules/nf-core/gatk4/haplotypecaller/main.nf +@@ -4,8 +4,8 @@ + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? +- 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': +- 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" ++ 'broadinstitute/gatk:4.6.0.0': ++ 'broadinstitute/gatk:4.6.0.0' }" + + input: + tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) + +'modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test.snap' is unchanged +'modules/nf-core/gatk4/haplotypecaller/tests/tags.yml' is unchanged +'modules/nf-core/gatk4/haplotypecaller/tests/main.nf.test' is unchanged +************************************************************ diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 3043ee07..f6ac46a2 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -4,8 +4,8 @@ process GATK4_HAPLOTYPECALLER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + 'broadinstitute/gatk:4.6.0.0': + 'broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) From fdef74389a9247c1724edd9413f3ff8bb4239d97 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 10 Sep 2024 14:06:20 +0200 Subject: [PATCH 2/4] pull from docker hub --- .../calibratedragstrmodel/gatk4-calibratedragstrmodel.diff | 4 ++-- modules/nf-core/gatk4/calibratedragstrmodel/main.nf | 4 ++-- .../gatk4/composestrtablefile/gatk4-composestrtablefile.diff | 4 ++-- modules/nf-core/gatk4/composestrtablefile/main.nf | 4 ++-- .../gatk4-createsequencedictionary.diff | 4 ++-- modules/nf-core/gatk4/createsequencedictionary/main.nf | 4 ++-- .../gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff | 4 ++-- modules/nf-core/gatk4/genomicsdbimport/main.nf | 4 ++-- modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff | 4 ++-- modules/nf-core/gatk4/genotypegvcfs/main.nf | 4 ++-- .../nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff | 4 ++-- modules/nf-core/gatk4/haplotypecaller/main.nf | 4 ++-- 12 files changed, 24 insertions(+), 24 deletions(-) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff b/modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff index cc4bba8c..e3b3aeff 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff +++ b/modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff @@ -10,8 +10,8 @@ Changes in 'gatk4/calibratedragstrmodel/main.nf': container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" -+ 'broadinstitute/gatk:4.6.0.0': -+ 'broadinstitute/gatk:4.6.0.0' }" ++ 'docker.io/broadinstitute/gatk:4.6.0.0': ++ 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(bam), path(bam_index) diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf index a09822be..49a315a0 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/main.nf +++ b/modules/nf-core/gatk4/calibratedragstrmodel/main.nf @@ -4,8 +4,8 @@ process GATK4_CALIBRATEDRAGSTRMODEL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'broadinstitute/gatk:4.6.0.0': - 'broadinstitute/gatk:4.6.0.0' }" + 'docker.io/broadinstitute/gatk:4.6.0.0': + 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(bam), path(bam_index) diff --git a/modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff b/modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff index b4b4d95d..3ebef227 100644 --- a/modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff +++ b/modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff @@ -10,8 +10,8 @@ Changes in 'gatk4/composestrtablefile/main.nf': container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" -+ 'broadinstitute/gatk:4.6.0.0': -+ 'broadinstitute/gatk:4.6.0.0' }" ++ 'docker.io/broadinstitute/gatk:4.6.0.0': ++ 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: path(fasta) diff --git a/modules/nf-core/gatk4/composestrtablefile/main.nf b/modules/nf-core/gatk4/composestrtablefile/main.nf index 2abda035..8be3f246 100644 --- a/modules/nf-core/gatk4/composestrtablefile/main.nf +++ b/modules/nf-core/gatk4/composestrtablefile/main.nf @@ -4,8 +4,8 @@ process GATK4_COMPOSESTRTABLEFILE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'broadinstitute/gatk:4.6.0.0': - 'broadinstitute/gatk:4.6.0.0' }" + 'docker.io/broadinstitute/gatk:4.6.0.0': + 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff b/modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff index ea62947f..538c05b1 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff +++ b/modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff @@ -10,8 +10,8 @@ Changes in 'gatk4/createsequencedictionary/main.nf': container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" -+ 'broadinstitute/gatk:4.6.0.0': -+ 'broadinstitute/gatk:4.6.0.0' }" ++ 'docker.io/broadinstitute/gatk:4.6.0.0': ++ 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/createsequencedictionary/main.nf b/modules/nf-core/gatk4/createsequencedictionary/main.nf index d03f98af..bb228fb3 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/main.nf +++ b/modules/nf-core/gatk4/createsequencedictionary/main.nf @@ -4,8 +4,8 @@ process GATK4_CREATESEQUENCEDICTIONARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'broadinstitute/gatk:4.6.0.0': - 'broadinstitute/gatk:4.6.0.0' }" + 'docker.io/broadinstitute/gatk:4.6.0.0': + 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff b/modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff index 2a94ac80..3dc446fe 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff +++ b/modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff @@ -10,8 +10,8 @@ Changes in 'gatk4/genomicsdbimport/main.nf': container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" -+ 'broadinstitute/gatk:4.6.0.0': -+ 'broadinstitute/gatk:4.6.0.0' }" ++ 'docker.io/broadinstitute/gatk:4.6.0.0': ++ 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genomicsdbimport/main.nf b/modules/nf-core/gatk4/genomicsdbimport/main.nf index 9c397744..d2230d34 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/main.nf +++ b/modules/nf-core/gatk4/genomicsdbimport/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOMICSDBIMPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'broadinstitute/gatk:4.6.0.0': - 'broadinstitute/gatk:4.6.0.0' }" + 'docker.io/broadinstitute/gatk:4.6.0.0': + 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(vcf), path(tbi), path(interval_file), val(interval_value), path(wspace) diff --git a/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff b/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff index 26e008be..71a907aa 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff +++ b/modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff @@ -10,8 +10,8 @@ Changes in 'gatk4/genotypegvcfs/main.nf': container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" -+ 'broadinstitute/gatk:4.6.0.0': -+ 'broadinstitute/gatk:4.6.0.0' }" ++ 'docker.io/broadinstitute/gatk:4.6.0.0': ++ 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/genotypegvcfs/main.nf b/modules/nf-core/gatk4/genotypegvcfs/main.nf index fe6e0d0d..c57d2d5a 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/main.nf +++ b/modules/nf-core/gatk4/genotypegvcfs/main.nf @@ -4,8 +4,8 @@ process GATK4_GENOTYPEGVCFS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'broadinstitute/gatk:4.6.0.0': - 'broadinstitute/gatk:4.6.0.0' }" + 'docker.io/broadinstitute/gatk:4.6.0.0': + 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(input), path(gvcf_index), path(intervals), path(intervals_index) diff --git a/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff b/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff index f284375a..1b807109 100644 --- a/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff +++ b/modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff @@ -10,8 +10,8 @@ Changes in 'gatk4/haplotypecaller/main.nf': container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" -+ 'broadinstitute/gatk:4.6.0.0': -+ 'broadinstitute/gatk:4.6.0.0' }" ++ 'docker.io/broadinstitute/gatk:4.6.0.0': ++ 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index f6ac46a2..5c7b8023 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -4,8 +4,8 @@ process GATK4_HAPLOTYPECALLER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'broadinstitute/gatk:4.6.0.0': - 'broadinstitute/gatk:4.6.0.0' }" + 'docker.io/broadinstitute/gatk:4.6.0.0': + 'docker.io/broadinstitute/gatk:4.6.0.0' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(dragstr_model) From a239c3a7197dbb0f61d74bced805091488699de8 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 10 Sep 2024 14:10:48 +0200 Subject: [PATCH 3/4] ignore igenomes by default --- nextflow.config | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow.config b/nextflow.config index 46e627fa..e392fd21 100644 --- a/nextflow.config +++ b/nextflow.config @@ -77,8 +77,8 @@ params { // References cmgg_config_base = "/conf/" - igenomes_base = null //'s3://ngi-igenomes/igenomes' - igenomes_ignore = false + igenomes_base = "null" //'s3://ngi-igenomes/igenomes' + igenomes_ignore = true genome = "GRCh38" genomes_base = "/references/" genomes_ignore = false From 9e3e51e57714dfda73e59620ed85c73846e2aa28 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 10 Sep 2024 14:14:01 +0200 Subject: [PATCH 4/4] prettier --- modules.json | 183 +++++++++++++-------------------------------------- 1 file changed, 46 insertions(+), 137 deletions(-) diff --git a/modules.json b/modules.json index 628b4ea9..48d7e9f0 100644 --- a/modules.json +++ b/modules.json @@ -8,299 +8,216 @@ "bcftools/annotate": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, "bcftools/concat": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/filter": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/norm": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/pluginscatter": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/query": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/stats": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/intersect": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "bedtools/split": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "ensemblvep/vep": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "gatk4/calibratedragstrmodel": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/calibratedragstrmodel/gatk4-calibratedragstrmodel.diff" }, "gatk4/composestrtablefile": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/composestrtablefile/gatk4-composestrtablefile.diff" }, "gatk4/createsequencedictionary": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/createsequencedictionary/gatk4-createsequencedictionary.diff" }, "gatk4/genomicsdbimport": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/genomicsdbimport/gatk4-genomicsdbimport.diff" }, "gatk4/genotypegvcfs": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/genotypegvcfs/gatk4-genotypegvcfs.diff" }, "gatk4/haplotypecaller": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/gatk4/haplotypecaller/gatk4-haplotypecaller.diff" }, "gawk": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mosdepth": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/format": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/pedfilter": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" }, "rtgtools/rocplot": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "rtgtools/vcfeval": { "branch": "master", "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/convert": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/index": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "somalier/extract": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "somalier/relate": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "tabix/bgzip": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules", - "vcf_annotate_ensemblvep_snpeff" - ] + "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"] }, "untar": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vardictjava": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcf2db": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "vcfanno": { "branch": "master", "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] } } }, @@ -309,33 +226,25 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "d20fb2a9cc3e2835e9d067d1046a63252eb17352", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "2fdce49d30c0254f76bc0f13c55c17455c1251ab", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfschema_plugin": { "branch": "master", "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "vcf_annotate_ensemblvep_snpeff": { "branch": "master", "git_sha": "cfd937a668919d948f6fcbf4218e79de50c2f36f", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +}