diff --git a/.github/tags.yml b/.github/tags.yml index ed5c9dcc..9fc74a2c 100644 --- a/.github/tags.yml +++ b/.github/tags.yml @@ -14,74 +14,66 @@ sra_to_samplesheet: # workflow: sra sra_custom_ena_metadata_fields: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_custom_ena_metadata_fields.nf.test sra_default_parameters: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_default_parameters.nf.test sra_force_sratools_download: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_force_sratools_download.nf.test sra_nf_core_pipeline_atacseq: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_nf_core_pipeline_atacseq.nf.test sra_nf_core_pipeline_rnaseq: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_nf_core_pipeline_rnaseq.nf.test sra_nf_core_pipeline_taxprofiler: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_nf_core_pipeline_taxprofiler.nf.test sra_nf_core_pipeline_viralrecon: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_nf_core_pipeline_viralrecon.nf.test sra_skip_fastq_download: - - conf/modules/sra.config - - modules/local/sra_ids_to_runinfo/main.nf - - modules/local/sra_runinfo_to_ftp/main.nf - - modules/local/sra_fastq_ftp/main.nf - - modules/local/sra_to_samplesheet/main.nf - - modules/local/sra_merge_samplesheet/main.nf - - workflows/sra/main.nf + - modules/local/sra_ids_to_runinfo/* + - modules/local/sra_runinfo_to_ftp/* + - modules/local/sra_fastq_ftp/* + - modules/local/sra_to_samplesheet/* + - modules/local/sra_merge_samplesheet/* + - workflows/sra/* - workflows/sra/tests/sra_skip_fastq_download.nf.test diff --git a/.github/workflows/cloud_tests_full.yml b/.github/workflows/cloud_tests_full.yml index e25a97aa..d0ed0552 100644 --- a/.github/workflows/cloud_tests_full.yml +++ b/.github/workflows/cloud_tests_full.yml @@ -27,7 +27,7 @@ jobs: compute_env: ${{ secrets.TOWER_CE_AWS_CPU }} workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}" run_name: "aws_fetchngs_full" - profiles: test_full,public_aws_ecr + profiles: test_full parameters: | { "hook_url": "${{ secrets.MEGATESTS_ALERTS_SLACK_HOOK_URL }}", diff --git a/.github/workflows/cloud_tests_small.yml b/.github/workflows/cloud_tests_small.yml index e7636fdc..12b8daab 100644 --- a/.github/workflows/cloud_tests_small.yml +++ b/.github/workflows/cloud_tests_small.yml @@ -25,7 +25,7 @@ jobs: compute_env: ${{ secrets.TOWER_CE_AWS_CPU }} workdir: "${{ secrets.TOWER_BUCKET_AWS }}/work/fetchngs/work-${{ github.sha }}" run_name: "aws_fetchngs_small" - profiles: test,public_aws_ecr + profiles: test parameters: | { "outdir": "${{ secrets.TOWER_BUCKET_AWS }}/fetchngs/results-test-${{ github.sha }}" diff --git a/CHANGELOG.md b/CHANGELOG.md index 20dd21f8..92e31da4 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -18,7 +18,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements ### Enhancements & fixes - [#166](https://github.com/nf-core/fetchngs/issues/175) - Add NF-TEST pipeline end-to-end tests for existing CI tests -- [#184](https://github.com/nf-core/fetchngs/pull/184/files) Emits all files in workflow for testing and enabling workflow to be imported (not supported by Nextflow) +- [#184](https://github.com/nf-core/fetchngs/pull/184) Emits all files in workflow for testing and enabling workflow to be imported (not supported by Nextflow) +- [#195](https://github.com/nf-core/fetchngs/pull/195) Separate configuration files for all modules ## [[1.10.0](https://github.com/nf-core/fetchngs/releases/tag/1.10.0)] - 2023-05-16 diff --git a/conf/base.config b/conf/base.config index 4767e522..6af79a7b 100644 --- a/conf/base.config +++ b/conf/base.config @@ -14,6 +14,12 @@ process { memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } + publishDir = [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + errorStrategy = { task.exitStatus in ((130..145) + 104) ? 'retry' : 'finish' } maxRetries = 1 maxErrors = '-1' @@ -57,7 +63,4 @@ process { errorStrategy = 'retry' maxRetries = 2 } - withName:CUSTOM_DUMPSOFTWAREVERSIONS { - cache = false - } } diff --git a/conf/modules/base.config b/conf/modules/base.config index d7eb6c86..035487c5 100644 --- a/conf/modules/base.config +++ b/conf/modules/base.config @@ -22,6 +22,7 @@ process { ] withName: CUSTOM_DUMPSOFTWAREVERSIONS { + cache = false publishDir = [ path: { "${params.outdir}/pipeline_info" }, mode: params.publish_dir_mode, diff --git a/conf/modules/sra.config b/conf/modules/sra.config deleted file mode 100644 index 15802b41..00000000 --- a/conf/modules/sra.config +++ /dev/null @@ -1,88 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config file for defining DSL2 per module options and publishing paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. ----------------------------------------------------------------------------------------- -*/ - -// -// Process options for the SRA workflow -// -process { - - withName: SRA_IDS_TO_RUNINFO { - publishDir = [ - path: { "${params.outdir}/metadata" }, - enabled: false - ] - } - - withName: SRA_RUNINFO_TO_FTP { - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SRA_FASTQ_FTP { - ext.args = '--retry 5 --continue-at - --max-time 1200' - publishDir = [ - [ - path: { "${params.outdir}/fastq" }, - mode: params.publish_dir_mode, - pattern: "*.fastq.gz" - ], - [ - path: { "${params.outdir}/fastq/md5" }, - mode: params.publish_dir_mode, - pattern: "*.md5" - ] - ] - } - - withName: SRATOOLS_PREFETCH { - publishDir = [ - path: { "${params.outdir}/sra" }, - enabled: false - ] - } - - withName: SRATOOLS_FASTERQDUMP { - ext.args = '--split-files --include-technical' - publishDir = [ - path: { "${params.outdir}/fastq" }, - mode: params.publish_dir_mode, - pattern: "*.fastq.gz" - ] - } - - withName: SRA_TO_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - enabled: false - ] - } - - withName: SRA_MERGE_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: MULTIQC_MAPPINGS_CONFIG { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - -} diff --git a/conf/modules/synapse.config b/conf/modules/synapse.config deleted file mode 100644 index 2f52aa6f..00000000 --- a/conf/modules/synapse.config +++ /dev/null @@ -1,66 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Config file for defining DSL2 per module options and publishing paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Available keys to override module options: - ext.args = Additional arguments appended to command in module. - ext.args2 = Second set of arguments appended to command in module (multi-tool modules). - ext.args3 = Third set of arguments appended to command in module (multi-tool modules). - ext.prefix = File name prefix for output files. ----------------------------------------------------------------------------------------- -*/ - -// -// Process options for the Synapse workflow -// - -process { - - withName: SYNAPSE_LIST { - ext.args = '--long' - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SYNAPSE_GET { - publishDir = [ - [ - path: { "${params.outdir}/fastq" }, - mode: params.publish_dir_mode, - pattern: "*.fastq.gz" - ], - [ - path: { "${params.outdir}/fastq/md5" }, - mode: params.publish_dir_mode, - pattern: "*.md5" - ] - ] - } - - withName: SYNAPSE_SHOW { - publishDir = [ - path: { "${params.outdir}/metadata" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - - withName: SYNAPSE_TO_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - enabled: false - ] - } - - withName: SYNAPSE_MERGE_SAMPLESHEET { - publishDir = [ - path: { "${params.outdir}/samplesheet" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } - ] - } - -} diff --git a/modules.json b/modules.json index 3137b88b..ab610dfb 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "05c280924b6c768d484c7c443dad5e605c4ff4b4", "installed_by": ["modules"] }, "custom/sratoolsncbisettings": { diff --git a/modules/local/multiqc_mappings_config/nextflow.config b/modules/local/multiqc_mappings_config/nextflow.config new file mode 100644 index 00000000..e2382930 --- /dev/null +++ b/modules/local/multiqc_mappings_config/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: 'MULTIQC_MAPPINGS_CONFIG' { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/sra_fastq_ftp/nextflow.config b/modules/local/sra_fastq_ftp/nextflow.config new file mode 100644 index 00000000..7b5ebf70 --- /dev/null +++ b/modules/local/sra_fastq_ftp/nextflow.config @@ -0,0 +1,17 @@ +process { + withName: 'SRA_FASTQ_FTP' { + ext.args = '--retry 5 --continue-at - --max-time 1200' + publishDir = [ + [ + path: { "${params.outdir}/fastq" }, + mode: params.publish_dir_mode, + pattern: "*.fastq.gz" + ], + [ + path: { "${params.outdir}/fastq/md5" }, + mode: params.publish_dir_mode, + pattern: "*.md5" + ] + ] + } +} diff --git a/modules/local/sra_ids_to_runinfo/nextflow.config b/modules/local/sra_ids_to_runinfo/nextflow.config new file mode 100644 index 00000000..73da969a --- /dev/null +++ b/modules/local/sra_ids_to_runinfo/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: 'SRA_IDS_TO_RUNINFO' { + publishDir = [ + path: { "${params.outdir}/metadata" }, + enabled: false + ] + } +} \ No newline at end of file diff --git a/modules/local/sra_merge_samplesheet/nextflow.config b/modules/local/sra_merge_samplesheet/nextflow.config new file mode 100644 index 00000000..f2926529 --- /dev/null +++ b/modules/local/sra_merge_samplesheet/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: 'SRA_MERGE_SAMPLESHEET' { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/sra_runinfo_to_ftp/nextflow.config b/modules/local/sra_runinfo_to_ftp/nextflow.config new file mode 100644 index 00000000..aee1848c --- /dev/null +++ b/modules/local/sra_runinfo_to_ftp/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: 'SRA_RUNINFO_TO_FTP' { + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/sra_to_samplesheet/nextflow.config b/modules/local/sra_to_samplesheet/nextflow.config new file mode 100644 index 00000000..da241c1a --- /dev/null +++ b/modules/local/sra_to_samplesheet/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: SRA_TO_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + enabled: false + ] + } +} diff --git a/modules/local/synapse_get/nextflow.config b/modules/local/synapse_get/nextflow.config new file mode 100644 index 00000000..869f80aa --- /dev/null +++ b/modules/local/synapse_get/nextflow.config @@ -0,0 +1,16 @@ +process { + withName: 'SYNAPSE_GET' { + publishDir = [ + [ + path: { "${params.outdir}/fastq" }, + mode: params.publish_dir_mode, + pattern: "*.fastq.gz" + ], + [ + path: { "${params.outdir}/fastq/md5" }, + mode: params.publish_dir_mode, + pattern: "*.md5" + ] + ] + } +} \ No newline at end of file diff --git a/modules/local/synapse_list/nextflow.config b/modules/local/synapse_list/nextflow.config new file mode 100644 index 00000000..15124234 --- /dev/null +++ b/modules/local/synapse_list/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: SYNAPSE_LIST { + ext.args = '--long' + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} diff --git a/modules/local/synapse_merge_samplesheet/nextflow.config b/modules/local/synapse_merge_samplesheet/nextflow.config new file mode 100644 index 00000000..9befef9c --- /dev/null +++ b/modules/local/synapse_merge_samplesheet/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: SYNAPSE_MERGE_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/synapse_show/nextflow.config b/modules/local/synapse_show/nextflow.config new file mode 100644 index 00000000..a1864dfe --- /dev/null +++ b/modules/local/synapse_show/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: 'SYNAPSE_SHOW' { + publishDir = [ + path: { "${params.outdir}/metadata" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } +} \ No newline at end of file diff --git a/modules/local/synapse_to_samplesheet/nextflow.config b/modules/local/synapse_to_samplesheet/nextflow.config new file mode 100644 index 00000000..b286c12c --- /dev/null +++ b/modules/local/synapse_to_samplesheet/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: SYNAPSE_TO_SAMPLESHEET { + publishDir = [ + path: { "${params.outdir}/samplesheet" }, + enabled: false + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc87273..c9d014b1 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "bioconda::multiqc=1.15" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.15--pyhdfd78af_0' : + 'biocontainers/multiqc:1.15--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/nextflow.config b/modules/nf-core/custom/dumpsoftwareversions/nextflow.config new file mode 100644 index 00000000..241654e7 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: CUSTOM_DUMPSOFTWAREVERSIONS { + cache = false + publishDir = [ + path: { "${params.outdir}/pipeline_info" }, + mode: params.publish_dir_mode, + pattern: '*_versions.yml' + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/sratoolsncbisettings/nextflow.config b/modules/nf-core/custom/sratoolsncbisettings/nextflow.config new file mode 100644 index 00000000..e69de29b diff --git a/modules/nf-core/sratools/fasterqdump/nextflow.config b/modules/nf-core/sratools/fasterqdump/nextflow.config new file mode 100644 index 00000000..f98b140d --- /dev/null +++ b/modules/nf-core/sratools/fasterqdump/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: SRATOOLS_FASTERQDUMP { + ext.args = '--split-files --include-technical' + publishDir = [ + path: { "${params.outdir}/fastq" }, + mode: params.publish_dir_mode, + pattern: "*.fastq.gz" + ] + } +} \ No newline at end of file diff --git a/modules/nf-core/sratools/prefetch/nextflow.config b/modules/nf-core/sratools/prefetch/nextflow.config new file mode 100644 index 00000000..a2ca8848 --- /dev/null +++ b/modules/nf-core/sratools/prefetch/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: SRATOOLS_PREFETCH { + publishDir = [ + path: { "${params.outdir}/sra" }, + enabled: false + ] + } +} \ No newline at end of file diff --git a/nextflow.config b/nextflow.config index e2584ce6..4fad92ca 100644 --- a/nextflow.config +++ b/nextflow.config @@ -216,14 +216,12 @@ manifest { doi = 'https://doi.org/10.5281/zenodo.5070524' } -// Load modules.config for DSL2 module specific options -includeConfig 'conf/modules/base.config' -if ( params.input_type == 'sra' ) { - includeConfig 'conf/modules/sra.config' -} -if ( params.input_type == 'synapse' ) { - includeConfig 'conf/modules/synapse.config' -} +// Module specific configs +// Currently just dumpsoftwareversions +includeConfig 'modules/nf-core/custom/dumpsoftwareversions/nextflow.config' + +// Workflow specific configs +includeConfig 'workflows/nextflow.config' // Function to ensure that resource requirements don't go beyond // a maximum limit diff --git a/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config new file mode 100644 index 00000000..996c1888 --- /dev/null +++ b/subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config @@ -0,0 +1,3 @@ +includeConfig '../../../modules/nf-core/sratools/prefetch/nextflow.config' +includeConfig '../../../modules/nf-core/sratools/fasterqdump/nextflow.config' +includeConfig '../../../modules/nf-core/custom/sratoolsncbisettings/nextflow.config' \ No newline at end of file diff --git a/workflows/nextflow.config b/workflows/nextflow.config new file mode 100644 index 00000000..d27deb3a --- /dev/null +++ b/workflows/nextflow.config @@ -0,0 +1,12 @@ +// Read in specific config relating to workflow. + +switch ( params.input_type ) { + case "sra": + includeConfig './sra/nextflow.config' + break + case "synapse": + includeConfig './synapse/nextflow.config' + break + default: + break +} \ No newline at end of file diff --git a/workflows/sra/nextflow.config b/workflows/sra/nextflow.config new file mode 100644 index 00000000..6b66fcd5 --- /dev/null +++ b/workflows/sra/nextflow.config @@ -0,0 +1,8 @@ +includeConfig "../../modules/local/multiqc_mappings_config/nextflow.config" +includeConfig "../../modules/local/sra_fastq_ftp/nextflow.config" +includeConfig "../../modules/local/sra_ids_to_runinfo/nextflow.config" +includeConfig "../../modules/local/sra_merge_samplesheet/nextflow.config" +includeConfig "../../modules/local/sra_runinfo_to_ftp/nextflow.config" +includeConfig "../../modules/local/sra_to_samplesheet/nextflow.config" +includeConfig "../../modules/nf-core/sratools/prefetch/nextflow.config" +includeConfig "../../subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/nextflow.config" diff --git a/workflows/synapse/nextflow.config b/workflows/synapse/nextflow.config new file mode 100644 index 00000000..01b71558 --- /dev/null +++ b/workflows/synapse/nextflow.config @@ -0,0 +1,5 @@ +includeConfig "../../modules/local/synapse_get/nextflow.config" +includeConfig "../../modules/local/synapse_to_samplesheet/nextflow.config" +includeConfig "../../modules/local/synapse_list/nextflow.config" +includeConfig "../../modules/local/synapse_merge_samplesheet/nextflow.config" +includeConfig "../../modules/local/synapse_show/nextflow.config" \ No newline at end of file