test CI

nf-core · Jan 10, 2025 · 31706f0 · 31706f0
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commit 31706f0
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -123,6 +123,24 @@ jobs:
       - name: Disk space cleanup
         uses: jlumbroso/[email protected]
 
+      - name: create references
+        id: references
+        run: |
+          mkdir tmp/
+          nextflow run nf-core/references -profile ${{ matrix.profile }} \
+          -r 8112ae8 \
+          --input https://raw.githubusercontent.com/nf-core/references-assets/41545a3631addaf491d22751b17607149b8512ac/assets/test/sarek/GRCh38_chr22.yml \
+          --tools bwamem1,createsequencedictionary,faidx,intervals,tabix \
+          --outdir ../references/
+          cd ..
+          rm -rf tmp/
+
+      - name: use references
+        id: references-use
+        run: |
+          nextflow run . -profile test,${{ matrix.profile }} --outdir results \
+          -params-file https://raw.githubusercontent.com/nf-core/references-assets/41545a3631addaf491d22751b17607149b8512ac/assets/test/sarek/GRCh38_chr22_params.yml
+
       - name: Start summary
         id: print-test
         run: |

diff --git a/main.nf b/main.nf
@@ -73,7 +73,6 @@ include { ANNOTATION_CACHE_INITIALISATION  } from './subworkflows/local/annotati
 include { DOWNLOAD_CACHE_SNPEFF_VEP        } from './subworkflows/local/download_cache_snpeff_vep'
 include { PIPELINE_COMPLETION              } from './subworkflows/local/utils_nfcore_sarek_pipeline'
 include { PIPELINE_INITIALISATION          } from './subworkflows/local/utils_nfcore_sarek_pipeline'
-include { PREPARE_GENOME                   } from './subworkflows/local/prepare_genome'
 include { PREPARE_INTERVALS                } from './subworkflows/local/prepare_intervals'
 include { PREPARE_REFERENCE_CNVKIT         } from './subworkflows/local/prepare_reference_cnvkit'
 
@@ -92,6 +91,12 @@ known_snps              = params.known_snps              ? Channel.fromPath(para
 mappability             = params.mappability             ? Channel.fromPath(params.mappability).collect()               : Channel.value([])
 pon                     = params.pon                     ? Channel.fromPath(params.pon).collect()                       : Channel.value([]) // PON is optional for Mutect2 (but highly recommended)
 sentieon_dnascope_model = params.sentieon_dnascope_model ? Channel.fromPath(params.sentieon_dnascope_model).collect()   : Channel.value([])
+msisensorpro_scan       = params.msisensorpro_scan       ? Channel.fromPath(params.msisensorpro_scan).collect()         : Channel.empty()
+allele_files            = params.allele_files            ? Channel.fromPath(params.allele_files).collect()              : Channel.empty()
+chr_files               = params.chr_files               ? Channel.fromPath(params.chr_files).collect()                 : Channel.empty()
+gc_file                 = params.gc_file                 ? Channel.fromPath(params.gc_file).collect()                   : Channel.empty()
+loci_files              = params.loci_files              ? Channel.fromPath(params.loci_files).collect()                : Channel.empty()
+rt_file                 = params.rt_file                 ? Channel.fromPath(params.rt_file).collect()                   : Channel.empty()
 
 // Initialize value channels based on params, defined in the params.genomes[params.genome] scope
 ascat_genome                = params.ascat_genome       ?:  Channel.empty()
@@ -104,6 +109,7 @@ vep_cache_version           = params.vep_cache_version  ?:  Channel.empty()
 vep_genome                  = params.vep_genome         ?:  Channel.empty()
 vep_species                 = params.vep_species        ?:  Channel.empty()
 
+
 vep_extra_files = []
 
 if (params.dbnsfp && params.dbnsfp_tbi) {
@@ -132,56 +138,26 @@ workflow NFCORE_SAREK {
     main:
     versions = Channel.empty()
 
-    // build indexes if needed
-    PREPARE_GENOME(
-        params.ascat_alleles,
-        params.ascat_loci,
-        params.ascat_loci_gc,
-        params.ascat_loci_rt,
-        bcftools_annotations,
-        params.chr_dir,
-        dbsnp,
-        fasta,
-        germline_resource,
-        known_indels,
-        known_snps,
-        pon)
-
     // Gather built indices or get them from the params
     // Built from the fasta file:
-    dict        = params.dict       ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect()
-                                    : PREPARE_GENOME.out.dict
-    fasta_fai   = params.fasta_fai  ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect()
-                                    : PREPARE_GENOME.out.fasta_fai
-    bwa         = params.bwa        ? Channel.fromPath(params.bwa).map{ it -> [ [id:'bwa'], it ] }.collect()
-                                    : PREPARE_GENOME.out.bwa
-    bwamem2     = params.bwamem2    ? Channel.fromPath(params.bwamem2).map{ it -> [ [id:'bwamem2'], it ] }.collect()
-                                    : PREPARE_GENOME.out.bwamem2
-    dragmap     = params.dragmap    ? Channel.fromPath(params.dragmap).map{ it -> [ [id:'dragmap'], it ] }.collect()
-                                    : PREPARE_GENOME.out.hashtable
+    dict        = params.dict      ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect()       : Channel.value([])
+    fasta_fai   = params.fasta_fai ? Channel.fromPath(params.fasta_fai).map{ it -> [ [id:'fai'], it ] }.collect()   : Channel.value([])
+    bwa         = params.bwa       ? Channel.fromPath(params.bwa).map{ it -> [ [id:'bwa'], it ] }.collect()         : Channel.empty()
+    bwamem2     = params.bwamem2   ? Channel.fromPath(params.bwamem2).map{ it -> [ [id:'bwamem2'], it ] }.collect() : Channel.empty()
+    dragmap     = params.dragmap   ? Channel.fromPath(params.dragmap).map{ it -> [ [id:'dragmap'], it ] }.collect() : Channel.empty()
 
     // Gather index for mapping given the chosen aligner
     index_alignment = (aligner == "bwa-mem" || aligner == "sentieon-bwamem") ? bwa :
         aligner == "bwa-mem2" ? bwamem2 :
         dragmap
 
-    // TODO: add a params for msisensorpro_scan
-    msisensorpro_scan      = PREPARE_GENOME.out.msisensorpro_scan
-
-    // For ASCAT, extracted from zip or tar.gz files
-    allele_files           = PREPARE_GENOME.out.allele_files
-    chr_files              = PREPARE_GENOME.out.chr_files
-    gc_file                = PREPARE_GENOME.out.gc_file
-    loci_files             = PREPARE_GENOME.out.loci_files
-    rt_file                = PREPARE_GENOME.out.rt_file
-
     // Tabix indexed vcf files
-    bcftools_annotations_tbi  = params.bcftools_annotations    ? params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : PREPARE_GENOME.out.bcftools_annotations_tbi : Channel.value([])
-    dbsnp_tbi                 = params.dbsnp                   ? params.dbsnp_tbi                ? Channel.fromPath(params.dbsnp_tbi).collect()                : PREPARE_GENOME.out.dbsnp_tbi                : Channel.value([])
-    germline_resource_tbi     = params.germline_resource       ? params.germline_resource_tbi    ? Channel.fromPath(params.germline_resource_tbi).collect()    : PREPARE_GENOME.out.germline_resource_tbi    : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
-    known_indels_tbi          = params.known_indels            ? params.known_indels_tbi         ? Channel.fromPath(params.known_indels_tbi).collect()         : PREPARE_GENOME.out.known_indels_tbi         : Channel.value([])
-    known_snps_tbi            = params.known_snps              ? params.known_snps_tbi           ? Channel.fromPath(params.known_snps_tbi).collect()           : PREPARE_GENOME.out.known_snps_tbi           : Channel.value([])
-    pon_tbi                   = params.pon                     ? params.pon_tbi                  ? Channel.fromPath(params.pon_tbi).collect()                  : PREPARE_GENOME.out.pon_tbi                  : Channel.value([])
+    bcftools_annotations_tbi  = params.bcftools_annotations && params.bcftools_annotations_tbi ? Channel.fromPath(params.bcftools_annotations_tbi).collect() : Channel.value([])
+    dbsnp_tbi                 = params.dbsnp                && params.dbsnp_tbi                ? Channel.fromPath(params.dbsnp_tbi).collect()                : Channel.value([])
+    germline_resource_tbi     = params.germline_resource    && params.germline_resource_tbi    ? Channel.fromPath(params.germline_resource_tbi).collect()    : [] //do not change to Channel.value([]), the check for its existence then fails for Getpileupsumamries
+    known_indels_tbi          = params.known_indels         && params.known_indels_tbi         ? Channel.fromPath(params.known_indels_tbi).collect()         : Channel.value([])
+    known_snps_tbi            = params.known_snps           && params.known_snps_tbi           ? Channel.fromPath(params.known_snps_tbi).collect()           : Channel.value([])
+    pon_tbi                   = params.pon                  && params.pon_tbi                  ? Channel.fromPath(params.pon_tbi).collect()                  : Channel.value([])
 
     // known_sites is made by grouping both the dbsnp and the known snps/indels resources
     // Which can either or both be optional
@@ -224,8 +200,8 @@ workflow NFCORE_SAREK {
     } else {
         cnvkit_reference = Channel.value([])
     }
+
     // Gather used softwares versions
-    versions = versions.mix(PREPARE_GENOME.out.versions)
     versions = versions.mix(PREPARE_INTERVALS.out.versions)
 
     vep_fasta = (params.vep_include_fasta) ? fasta.map{ fasta -> [ [ id:fasta.baseName ], fasta ] } : [[id: 'null'], []]

diff --git a/subworkflows/local/prepare_genome/main.nf b/subworkflows/local/prepare_genome/main.nf