diff --git a/modules.json b/modules.json index 9693296c..48d7e9f0 100644 --- a/modules.json +++ b/modules.json @@ -79,32 +79,38 @@ "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", 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..e3b3aeff --- /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' }" ++ '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) + +'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..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 ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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 new file mode 100644 index 00000000..3ebef227 --- /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' }" ++ 'docker.io/broadinstitute/gatk:4.6.0.0': ++ 'docker.io/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..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 ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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 new file mode 100644 index 00000000..538c05b1 --- /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' }" ++ 'docker.io/broadinstitute/gatk:4.6.0.0': ++ 'docker.io/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..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 ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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 new file mode 100644 index 00000000..3dc446fe --- /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' }" ++ '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) + +'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..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 ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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 new file mode 100644 index 00000000..71a907aa --- /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' }" ++ '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) + +'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..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 ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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 new file mode 100644 index 00000000..1b807109 --- /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' }" ++ '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) + +'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..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 ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': - 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_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)