Refactor

.github/workflows/download_pipeline.yml

@@ -69,11 +69,3 @@ jobs:
 
       - name: Inspect download
         run: tree ./${{ env.REPOTITLE_LOWERCASE }}
-
-      - name: Run the downloaded pipeline (stub)
-        id: stub_run_pipeline
-        continue-on-error: true
-        env:
-          NXF_SINGULARITY_CACHEDIR: ./
-          NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results

CHANGELOG.md

@@ -7,12 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- A new parameter `skip_smncopynumbercaller` to skip smncopynumbercaller module[#574](https://github.com/nf-core/raredisease/pull/574)
 - A new parameter `skip_sv_calling` to skip sv calling workflow [#572](https://github.com/nf-core/raredisease/pull/572)
 - Two new parameters `skip_snv_calling` and `skip_repeat_analysis` to skip snv calling and repeat analysis respectively [#571](https://github.com/nf-core/raredisease/pull/571)
 - Two new parameters `mbuffer_mem` and `samtools_sort_threads` to control resources given to mbuffer and samtools sort in the bwameme module [#570](https://github.com/nf-core/raredisease/pull/570)
 
 ### `Changed`
 
+- Remove several skip parameters that had been included in the pipeline to avoid failed CI tests (see parameters table below) [#574](https://github.com/nf-core/raredisease/pull/574)
 - `readcount_intervals` parameter is now mandatory for running germlinecnvcaller. [#570](https://github.com/nf-core/raredisease/pull/570)
 - Turn off CNVnator, TIDDIT, SMNCopyNumberCaller, Gens, and Vcf2cytosure for targeted analysis [#573](https://github.com/nf-core/raredisease/pull/573)
 
@@ -23,13 +25,18 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Parameters
 
-| Old parameter | New parameter         |
-| ------------- | --------------------- |
-|               | mbuffer_mem           |
-|               | samtools_sort_threads |
-|               | skip_repeat_analysis  |
-|               | skip_snv_calling      |
-|               | skip_sv_calling       |
+| Old parameter   | New parameter            |
+| --------------- | ------------------------ |
+|                 | mbuffer_mem              |
+|                 | samtools_sort_threads    |
+|                 | skip_repeat_analysis     |
+|                 | skip_snv_calling         |
+|                 | skip_sv_calling          |
+| skip_eklipse    |                          |
+| skip_fastqc     |                          |
+| skip_haplocheck |                          |
+| skip_qualimap   |                          |
+|                 | skip_smncopynumbercaller |
 
 ## 2.1.0 - Obelix [2024-05-29]
 

conf/modules/qc_bam.config

@@ -35,10 +35,8 @@ process {
         ext.prefix = { "${meta.id}_hsmetrics" }
     }
 
-    if (!params.skip_qualimap) {
-        withName: '.*QC_BAM:QUALIMAP_BAMQC' {
-            ext.prefix = { "${meta.id}_qualimap" }
-        }
+    withName: '.*QC_BAM:QUALIMAP_BAMQC' {
+        ext.prefix = { "${meta.id}_qualimap" }
     }
 
     withName: '.*QC_BAM:TIDDIT_COV' {

conf/test.config

@@ -24,11 +24,7 @@ params {
     mito_name       = 'MT'
 
     // analysis params
-    skip_eklipse           = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip tool on Github CI
-    skip_fastqc            = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip tool on Github CI
     skip_germlinecnvcaller = true
-    skip_haplocheck        = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip tool on Github CI
-    skip_qualimap          = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip tool on Github CI
     skip_mt_annotation     = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip annotation on Github CI
     skip_mt_subsample      = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip subsample on Github CI
     skip_peddy             = true

conf/test_one_sample.config

@@ -24,11 +24,7 @@ params {
     mito_name       = 'MT'
 
     // analysis params
-    skip_eklipse           = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip tool on Github CI
-    skip_fastqc            = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip tool on Github CI
     skip_germlinecnvcaller = true
-    skip_haplocheck        = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip tool on Github CI
-    skip_qualimap          = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip tool on Github CI
     skip_mt_annotation     = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip annotation on Github CI
     skip_mt_subsample      = System.getenv("GITHUB_ACTIONS").equals(null) ? false : true // skip subsample on Github CI
     skip_peddy             = true

nextflow.config

@@ -27,18 +27,15 @@ params {
     run_mt_for_wes             = false
     run_rtgvcfeval             = false
     save_mapped_as_cram        = false
-    skip_eklipse               = false
     skip_fastp                 = false
-    skip_fastqc                = false
     skip_gens                  = true
     skip_germlinecnvcaller     = false
-    skip_haplocheck            = false
     skip_peddy                 = false
     skip_me_calling            = false
     skip_me_annotation         = false
     skip_mt_annotation         = false
-    skip_qualimap              = false
     skip_repeat_analysis       = false
+    skip_smncopynumbercaller   = false
     skip_snv_annotation        = false
     skip_snv_calling           = false
     skip_sv_annotation         = false

nextflow_schema.json

@@ -508,21 +508,11 @@
                     "description": "Specifies whether to generate and publish alignment files as cram instead of bam",
                     "fa_icon": "fas fa-toggle-on"
                 },
-                "skip_fastqc": {
-                    "type": "boolean",
-                    "description": "Specifies whether or not to skip FASTQC.",
-                    "fa_icon": "fas fa-toggle-on"
-                },
                 "skip_fastp": {
                     "type": "boolean",
                     "description": "Specifies whether or not to skip trimming with fastp.",
                     "fa_icon": "fas fa-toggle-on"
                 },
-                "skip_haplocheck": {
-                    "type": "boolean",
-                    "description": "Specifies whether or not to skip haplocheck.",
-                    "fa_icon": "fas fa-toggle-on"
-                },
                 "skip_gens": {
                     "type": "boolean",
                     "description": "Specifies whether or not to skip gens preprocessing subworkflow.",
@@ -533,21 +523,11 @@
                     "description": "Specifies whether or not to skip CNV calling using GATK's GermlineCNVCaller",
                     "fa_icon": "fas fa-toggle-on"
                 },
-                "skip_eklipse": {
-                    "type": "boolean",
-                    "description": "Specifies whether or not to skip eKLIPse.",
-                    "fa_icon": "fas fa-toggle-on"
-                },
                 "skip_peddy": {
                     "type": "boolean",
                     "description": "Specifies whether or not to skip peddy.",
                     "fa_icon": "fas fa-toggle-on"
                 },
-                "skip_qualimap": {
-                    "type": "boolean",
-                    "description": "Specifies whether or not to skip Qualimap.",
-                    "fa_icon": "fas fa-toggle-on"
-                },
                 "skip_me_calling": {
                     "type": "boolean",
                     "description": "Specifies whether or not to skip calling mobile elements, and the subsequent annotation step.",
@@ -573,6 +553,11 @@
                     "description": "Specifies whether or not to skip calling and annotation of repeat expansions.",
                     "fa_icon": "fas fa-toggle-on"
                 },
+                "skip_smncopynumbercaller": {
+                    "type": "boolean",
+                    "description": "Specifies whether or not to skip smncopynumbercaller.",
+                    "fa_icon": "fas fa-toggle-on"
+                },
                 "skip_snv_annotation": {
                     "type": "boolean",
                     "description": "Specifies whether or not to skip annotate SNV subworkflow.",

subworkflows/local/qc_bam.nf

@@ -45,10 +45,8 @@ workflow QC_BAM {
 
         PICARD_COLLECTHSMETRICS (ch_hsmetrics_in, ch_genome_fasta, ch_genome_fai, [[],[]])
 
-        if (!params.skip_qualimap) {
-            ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results
-            ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first())
-        }
+        ch_qualimap = QUALIMAP_BAMQC (ch_bam, []).results
+        ch_versions = ch_versions.mix(QUALIMAP_BAMQC.out.versions.first())
 
         TIDDIT_COV (ch_bam, [[],[]]) // 2nd pos. arg is req. only for cram input
 

subworkflows/local/utils_nfcore_raredisease_pipeline/main.nf

@@ -224,12 +224,12 @@ def toolCitationText() {
     variant_call_text = [
         params.variant_caller.equals("deepvariant") ? "DeepVariant (Poplin et al., 2018)," : "",
         params.variant_caller.equals("sentieon") ? "Sentieon DNAscope (Freed et al., 2022)," : "",
-        params.skip_haplocheck ? "" : "Haplocheck (Weissensteiner et al., 2021),",
+        "Haplocheck (Weissensteiner et al., 2021),",
         "CNVnator (Abyzov et al., 2011),",
         "TIDDIT (Eisfeldt et al., 2017),",
         "Manta (Chen et al., 2016),",
         "GLnexus (Yun et al., 2021),",
-        params.skip_eklipse ? "" : "eKLIPse (Goudenge et al., 2019),",
+        "eKLIPse (Goudenge et al., 2019),",
     ]
     repeat_call_text = [
         "ExpansionHunter (Dolzhenko et al., 2019),",
@@ -278,7 +278,7 @@ def toolCitationText() {
         "RetroSeq (Keane et al., 2013),",
     ]
     preprocessing_text = [
-        params.skip_fastqc ? "" : "FastQC (Andrews 2010),",
+        "FastQC (Andrews 2010),",
         params.skip_fastp  ? "" : "Fastp (Chen, 2023),",
     ]
     other_citation_text = [
@@ -333,12 +333,12 @@ def toolBibliographyText() {
     variant_call_text = [
         params.variant_caller.equals("deepvariant") ? "<li>Poplin, R., Chang, P.-C., Alexander, D., Schwartz, S., Colthurst, T., Ku, A., Newburger, D., Dijamco, J., Nguyen, N., Afshar, P. T., Gross, S. S., Dorfman, L., McLean, C. Y., & DePristo, M. A. (2018). A universal SNP and small-indel variant caller using deep neural networks. Nature Biotechnology, 36(10), 983–987. https://doi.org/10.1038/nbt.4235</li>" : "",
         params.variant_caller.equals("sentieon") ? "<li>Freed, D., Pan, R., Chen, H., Li, Z., Hu, J., & Aldana, R. (2022). DNAscope: High accuracy small variant calling using machine learning [Preprint]. Bioinformatics. https://doi.org/10.1101/2022.05.20.492556</li>" : "",
-        params.skip_haplocheck ? "" : "<li>Weissensteiner, H., Forer, L., Fendt, L., Kheirkhah, A., Salas, A., Kronenberg, F., & Schoenherr, S. (2021). Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Research, 31(2), 309–316. https://doi.org/10.1101/gr.256545.119</li>",
+        "<li>Weissensteiner, H., Forer, L., Fendt, L., Kheirkhah, A., Salas, A., Kronenberg, F., & Schoenherr, S. (2021). Contamination detection in sequencing studies using the mitochondrial phylogeny. Genome Research, 31(2), 309–316. https://doi.org/10.1101/gr.256545.119</li>",
         "<li>Abyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011). CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Research, 21(6), 974–984. https://doi.org/10.1101/gr.114876.110</li>",
         "<li>Eisfeldt, J., Vezzi, F., Olason, P., Nilsson, D., & Lindstrand, A. (2017). TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data. F1000Research, 6, 664. https://doi.org/10.12688/f1000research.11168.2</li>",
         "<li>Chen, X., Schulz-Trieglaff, O., Shaw, R., Barnes, B., Schlesinger, F., Källberg, M., Cox, A. J., Kruglyak, S., & Saunders, C. T. (2016). Manta: Rapid detection of structural variants and indels for germline and cancer sequencing applications. Bioinformatics, 32(8), 1220–1222. https://doi.org/10.1093/bioinformatics/btv710</li>",
         "<li>Yun, T., Li, H., Chang, P.-C., Lin, M. F., Carroll, A., & McLean, C. Y. (2021). Accurate, scalable cohort variant calls using DeepVariant and GLnexus. Bioinformatics, 36(24), 5582–5589. https://doi.org/10.1093/bioinformatics/btaa1081</li>",
-        params.skip_eklipse ? "" : "<li>Goudenège, D., Bris, C., Hoffmann, V., Desquiret-Dumas, V., Jardel, C., Rucheton, B., Bannwarth, S., Paquis-Flucklinger, V., Lebre, A. S., Colin, E., Amati-Bonneau, P., Bonneau, D., Reynier, P., Lenaers, G., & Procaccio, V. (2019). eKLIPse: A sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genetics in Medicine, 21(6), 1407–1416. https://doi.org/10.1038/s41436-018-0350-8</li>",
+        "<li>Goudenège, D., Bris, C., Hoffmann, V., Desquiret-Dumas, V., Jardel, C., Rucheton, B., Bannwarth, S., Paquis-Flucklinger, V., Lebre, A. S., Colin, E., Amati-Bonneau, P., Bonneau, D., Reynier, P., Lenaers, G., & Procaccio, V. (2019). eKLIPse: A sensitive tool for the detection and quantification of mitochondrial DNA deletions from next-generation sequencing data. Genetics in Medicine, 21(6), 1407–1416. https://doi.org/10.1038/s41436-018-0350-8</li>",
     ]
     repeat_call_text = [
         "<li>Dolzhenko, E., Deshpande, V., Schlesinger, F., Krusche, P., Petrovski, R., Chen, S., Emig-Agius, D., Gross, A., Narzisi, G., Bowman, B., Scheffler, K., van Vugt, J. J. F. A., French, C., Sanchis-Juan, A., Ibáñez, K., Tucci, A., Lajoie, B. R., Veldink, J. H., Raymond, F. L., … Eberle, M. A. (2019). ExpansionHunter: A sequence-graph-based tool to analyze variation in short tandem repeat regions. Bioinformatics, 35(22), 4754–4756. https://doi.org/10.1093/bioinformatics/btz431</li>",
@@ -389,7 +389,7 @@ def toolBibliographyText() {
         "<li>Keane, T. M., Wong, K., & Adams, D. J. (2013). RetroSeq: Transposable element discovery from next-generation sequencing data. Bioinformatics, 29(3), 389–390. https://doi.org/10.1093/bioinformatics/bts697</li>",
     ]
     preprocessing_text = [
-        params.skip_fastqc ? "" : "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</li>",
+        "<li>Andrews S, (2010) FastQC, URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/</li>",
         params.skip_fastp  ? "" : "<li>Chen, S. (2023). Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp. iMeta, 2(2), e107. https://doi.org/10.1002/imt2.107</li>",
     ]
     other_citation_text = [

subworkflows/local/variant_calling/call_snv_MT.nf

@@ -23,12 +23,10 @@ workflow CALL_SNV_MT {
 
         GATK4_MUTECT2_MT (ch_bam_bai_int, ch_fasta, ch_fai, ch_dict, [], [], [],[])
 
-        if (!params.skip_haplocheck) {
-            HAPLOCHECK_MT (GATK4_MUTECT2_MT.out.vcf).set { ch_haplocheck }
-            ch_versions = ch_versions.mix(HAPLOCHECK_MT.out.versions.first())
-            ch_haplocheck_txt  = HAPLOCHECK_MT.out.txt
-            ch_haplocheck_html = HAPLOCHECK_MT.out.html
-        }
+        HAPLOCHECK_MT (GATK4_MUTECT2_MT.out.vcf).set { ch_haplocheck }
+        ch_versions = ch_versions.mix(HAPLOCHECK_MT.out.versions.first())
+        ch_haplocheck_txt  = HAPLOCHECK_MT.out.txt
+        ch_haplocheck_html = HAPLOCHECK_MT.out.html
 
         // Filter Mutect2 calls
         ch_mutect_vcf = GATK4_MUTECT2_MT.out.vcf.join(GATK4_MUTECT2_MT.out.tbi, failOnMismatch:true, failOnDuplicate:true)

subworkflows/local/variant_calling/call_sv_MT.nf

@@ -16,13 +16,11 @@ workflow CALL_SV_MT {
         ch_eklipse_genes  = Channel.empty()
         ch_eklipse_circos = Channel.empty()
 
-        if (!params.skip_eklipse){
-            EKLIPSE(ch_bam_bai,[])
-            ch_eklipse_del    = EKLIPSE.out.deletions
-            ch_eklipse_genes  = EKLIPSE.out.genes
-            ch_eklipse_circos = EKLIPSE.out.circos
-            ch_versions = ch_versions.mix(EKLIPSE.out.versions.first())
-        }
+        EKLIPSE(ch_bam_bai,[])
+        ch_eklipse_del    = EKLIPSE.out.deletions
+        ch_eklipse_genes  = EKLIPSE.out.genes
+        ch_eklipse_circos = EKLIPSE.out.circos
+        ch_versions = ch_versions.mix(EKLIPSE.out.versions.first())
 
         MT_DELETION(ch_bam_bai, ch_fasta)
 

workflows/raredisease.nf

@@ -90,6 +90,9 @@ if (!params.skip_gens) {
     mandatoryParams += ["gens_gnomad_pos", "gens_interval_list", "gens_pon_female", "gens_pon_male"]
 }
 
+if (!params.skip_smncopynumbercaller) {
+    mandatoryParams += ["genome"]
+}
 for (param in mandatoryParams.unique()) {
     if (params[param] == null) {
         println("params." + param + " not set.")
@@ -370,10 +373,8 @@ workflow RAREDISEASE {
     //
     // Input QC
     //
-    if (!params.skip_fastqc) {
-        FASTQC (ch_samplesheet)
-        ch_versions = ch_versions.mix(FASTQC.out.versions.first())
-    }
+    FASTQC (ch_samplesheet)
+    ch_versions = ch_versions.mix(FASTQC.out.versions.first())
 
     //
     // Create chromosome bed and intervals for splitting and gathering operations
@@ -695,7 +696,7 @@ workflow RAREDISEASE {
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 */
 
-    if ( params.analysis_type.equals("wgs") ) {
+    if ( params.analysis_type.equals("wgs") && !params.skip_smncopynumbercaller ) {
         RENAME_BAM_FOR_SMNCALLER(ch_mapped.genome_marked_bam, "bam").output
             .collect{it}
             .toList()
@@ -830,9 +831,7 @@ workflow RAREDISEASE {
         )
     )
 
-    if (!params.skip_fastqc) {
-        ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
-    }
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.multiple_metrics.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.hs_metrics.map{it[1]}.collect().ifEmpty([]))
     ch_multiqc_files = ch_multiqc_files.mix(QC_BAM.out.qualimap_results.map{it[1]}.collect().ifEmpty([]))