diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index c6c9ae459c5..12d201a5d51 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -644,6 +644,12 @@ jobs: path: modules/nf-core/parabricks/fq2bammeth - profile: singularity path: modules/nf-core/parabricks/fq2bammeth + - profile: conda + path: modules/nf-core/parabricks/fq2bam + - profile: docker_self_hosted + path: modules/nf-core/parabricks/fq2bam + - profile: singularity + path: modules/nf-core/parabricks/fq2bam - profile: conda path: subworkflows/nf-core/vcf_annotate_ensemblvep - profile: conda diff --git a/modules/nf-core/parabricks/fq2bam/meta.yml b/modules/nf-core/parabricks/fq2bam/meta.yml index bd7e8bd773c..b1cae9c4fa4 100644 --- a/modules/nf-core/parabricks/fq2bam/meta.yml +++ b/modules/nf-core/parabricks/fq2bam/meta.yml @@ -24,11 +24,6 @@ input: type: file description: fastq.gz files pattern: "*.fastq.gz" - - interval_file: - type: file - description: (optional) file(s) containing genomic intervals for use in base - quality score recalibration (BQSR) - pattern: "*.{bed,interval_list,picard,list,intervals}" - - meta2: type: map description: | @@ -45,6 +40,11 @@ input: type: file description: reference BWA index pattern: "*.{amb,ann,bwt,pac,sa}" + - - interval_file: + type: file + description: (optional) file(s) containing genomic intervals for use in base + quality score recalibration (BQSR) + pattern: "*.{bed,interval_list,picard,list,intervals}" - - known_sites: type: file description: (optional) known sites file(s) for calculating BQSR. markdups must diff --git a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test index 646baf1ac98..46d06322c32 100644 --- a/modules/nf-core/parabricks/fq2bam/tests/main.nf.test +++ b/modules/nf-core/parabricks/fq2bam/tests/main.nf.test @@ -5,6 +5,12 @@ nextflow_process { process "PARABRICKS_FQ2BAM" config "./nextflow.config" + tag "bwa/index" + tag "modules" + tag "parabricks/fq2bam" + tag "modules_nfcore" + tag "parabricks" + setup { run("BWA_INDEX") { script "../../../bwa/index/main.nf"