Merge pull request #1648 from nf-core/refactor-sra-fastq

refactor: rename and update subworkflow

subworkflows/nf-core/sra_fastq/main.nf

@@ -1,34 +0,0 @@
-//
-// Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
-//
-
-params.prefetch_options    = [:]
-params.fasterqdump_options = [:]
-
-include { SRATOOLS_PREFETCH    } from '../../../modules/sratools/prefetch/main'    addParams( options: params.prefetch_options    )
-include { SRATOOLS_FASTERQDUMP } from '../../../modules/sratools/fasterqdump/main' addParams( options: params.fasterqdump_options )
-
-workflow SRA_FASTQ {
-    take:
-    sra_ids  // channel: [ val(meta), val(id) ]
-
-    main:
-
-    ch_versions = Channel.empty()
-
-    //
-    // Prefetch sequencing reads in SRA format.
-    //
-    SRATOOLS_PREFETCH ( sra_ids )
-    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
-
-    //
-    // Convert the SRA format into one or more compressed FASTQ files.
-    //
-    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra )
-    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
-
-    emit:
-    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
-    versions = ch_versions                     // channel: [ versions.yml ]
-}

subworkflows/nf-core/srafastq/main.nf

@@ -0,0 +1,38 @@
+include { CUSTOM_SRATOOLSNCBISETTINGS } from '../../../modules/custom/sratoolsncbisettings/main'
+include { SRATOOLS_PREFETCH           } from '../../../modules/sratools/prefetch/main'
+include { SRATOOLS_FASTERQDUMP        } from '../../../modules/sratools/fasterqdump/main'
+
+/**
+ * Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
+ */
+workflow SRAFASTQ {
+    take:
+    sra_ids  // channel: [ val(meta), val(id) ]
+
+    main:
+
+    ch_versions = Channel.empty()
+
+    //
+    // Detect existing NCBI user settings or create new ones.
+    //
+    CUSTOM_SRATOOLSNCBISETTINGS()
+    def settings = CUSTOM_SRATOOLSNCBISETTINGS.out.ncbi_settings
+    ch_versions = ch_versions.mix( CUSTOM_SRATOOLSNCBISETTINGS.out.versions )
+
+    //
+    // Prefetch sequencing reads in SRA format.
+    //
+    SRATOOLS_PREFETCH ( sra_ids, settings )
+    ch_versions = ch_versions.mix( SRATOOLS_PREFETCH.out.versions.first() )
+
+    //
+    // Convert the SRA format into one or more compressed FASTQ files.
+    //
+    SRATOOLS_FASTERQDUMP ( SRATOOLS_PREFETCH.out.sra, settings )
+    ch_versions = ch_versions.mix( SRATOOLS_FASTERQDUMP.out.versions.first() )
+
+    emit:
+    reads    = SRATOOLS_FASTERQDUMP.out.reads  // channel: [ val(meta), [ reads ] ]
+    versions = ch_versions                     // channel: [ versions.yml ]
+}

subworkflows/nf-core/srafastq/meta.yml

@@ -1,11 +1,14 @@
 name: sra_fastq
 description: Download FASTQ sequencing reads from the NCBI's Sequence Read Archive (SRA).
 keywords:
+  - SRA
+  - NCBI
   - sequencing
   - FASTQ
   - prefetch
-  - dump
+  - fasterq-dump
 modules:
+  - custom/sratoolsncbisettings
   - sratools/prefetch
   - sratools/fasterqdump
 input:
@@ -17,7 +20,7 @@ input:
   - id:
       type: string
       description: >
-        SRA identifier.
+        SRA run identifier.
 # TODO Update when we decide on a standard for subworkflow docs
 output:
   - meta:

tests/subworkflows/nf-core/sra_fastq/main.nf

@@ -1,23 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SRA_FASTQ } from '../../../../subworkflows/nf-core/sra_fastq/main.nf' addParams( [:] )
-
-workflow test_sra_fastq_single_end {
-    input = [
-        [ id:'test_single_end', single_end:true ], // meta map
-        'SRR13255544'
-    ]
-
-    SRA_FASTQ ( input )
-}
-
-workflow test_sra_fastq_paired_end {
-    input = [
-        [ id:'test_paired_end', single_end:false ], // meta map
-        'SRR11140744'
-    ]
-
-    SRA_FASTQ ( input )
-}

tests/subworkflows/nf-core/sra_fastq/test.yml

@@ -1,27 +0,0 @@
-- name: sra fastq single-end
-  command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_single_end -c tests/config/nextflow.config
-  tags:
-    - subworkflows
-    # - subworkflows/sra_fastq
-    # Modules
-    # - sratools
-    # - sratools/prefetch
-    # - sratools/fasterqdump
-  files:
-    - path: output/sratools/SRR13255544.fastq.gz
-      md5sum: 1054c7b71884acdb5eed8a378f18be82
-
-- name: sra fastq paired-end
-  command: nextflow run ./tests/subworkflows/nf-core/sra_fastq -entry test_sra_fastq_paired_end -c tests/config/nextflow.config
-  tags:
-    - subworkflows
-    # - subworkflows/sra_fastq
-    # Modules
-    # - sratools
-    # - sratools/prefetch
-    # - sratools/fasterqdump
-  files:
-    - path: output/sratools/SRR11140744_1.fastq.gz
-      md5sum: 193809c784a4ea132ab2a253fa4f55b6
-    - path: output/sratools/SRR11140744_2.fastq.gz
-      md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e

tests/subworkflows/nf-core/srafastq/main.nf

@@ -0,0 +1,29 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SRAFASTQ } from '../../../../subworkflows/nf-core/srafastq/main.nf'
+
+workflow test_srafastq_single_end {
+    input = Channel.of(
+        [
+            [ id:'test_single_end1', single_end:true ], // meta map
+            'DRR000774'
+        ],
+        [
+            [ id:'test_single_end2', single_end:true ], // meta map
+            'DRR000775'
+        ]
+    )
+
+    SRAFASTQ ( input )
+}
+
+workflow test_srafastq_paired_end {
+    input = [
+        [ id:'test_paired_end', single_end:false ], // meta map
+        'SRR11140744'
+    ]
+
+    SRAFASTQ ( input )
+}

tests/subworkflows/nf-core/srafastq/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+
+}

tests/subworkflows/nf-core/srafastq/test.yml

@@ -0,0 +1,29 @@
+- name: srafastq single-end
+  command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_single_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/srafastq
+    # Modules
+    # - sratools
+    # - sratools/prefetch
+    # - sratools/fasterqdump
+  files:
+    - path: output/sratools/DRR000774.fastq.gz
+      md5sum: 19029a1132115b55277a0d79ee089b49
+    - path: output/sratools/DRR000775.fastq.gz
+      md5sum: 59ff24c86ecb260752668c059c2a1eaf
+
+- name: srafastq paired-end
+  command: nextflow run ./tests/subworkflows/nf-core/srafastq -entry test_srafastq_paired_end -c tests/config/nextflow.config -c tests/subworkflows/nf-core/srafastq/nextflow.config
+  tags:
+    - subworkflows
+    # - subworkflows/srafastq
+    # Modules
+    # - sratools
+    # - sratools/prefetch
+    # - sratools/fasterqdump
+  files:
+    - path: output/sratools/SRR11140744_1.fastq.gz
+      md5sum: 193809c784a4ea132ab2a253fa4f55b6
+    - path: output/sratools/SRR11140744_2.fastq.gz
+      md5sum: 3e3b3af3413f50a1685fd7b3f1456d4e