Update to match hello-modules

This should make the transition to a deployed pipeline more obvious to an observer
seqeralabs · Nov 5, 2024 · cd9fbd7 · cd9fbd7
1 parent 3f6792e
commit cd9fbd7
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Showing 7 changed files with 215 additions and 158 deletions.
diff --git a/main.nf b/main.nf
@@ -1,156 +1,11 @@
 #!/usr/bin/env nextflow
 
-/*
- * Pipeline parameters
- */
-
-// Primary input (file of input files, one per line)
-params.reads_bam = "${projectDir}/data/sample_bams.txt"
-
-// Accessory files
-params.reference        = "${projectDir}/data/ref/ref.fasta"
-params.reference_index  = "${projectDir}/data/ref/ref.fasta.fai"
-params.reference_dict   = "${projectDir}/data/ref/ref.dict"
-params.intervals        = "${projectDir}/data/ref/intervals.bed"
-
-// Base name for final output file
-params.cohort_name = "family_trio"
-
-params.outdir = "results"
-
-/*
- * Generate BAM index file
- */
-process SAMTOOLS_INDEX {
-
-    container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464'
-
-    publishDir "$params.outdir", mode: 'symlink'
-
-    input:
-        path input_bam
-
-    output:
-        tuple path(input_bam), path("${input_bam}.bai")
-
-    """
-    samtools index '$input_bam'
-    """
-}
-
-/*
- * Call variants with GATK HaplotypeCaller
- */
-process GATK_HAPLOTYPECALLER {
-
-    container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"
-
-    publishDir "$params.outdir", mode: 'symlink'
-
-    input:
-        tuple path(input_bam), path(input_bam_index)
-        path ref_fasta
-        path ref_index
-        path ref_dict
-        path interval_list
-
-    output:
-        path "${input_bam}.g.vcf"
-        path "${input_bam}.g.vcf.idx"
-
-    """
-    gatk HaplotypeCaller \
-        -R ${ref_fasta} \
-        -I ${input_bam} \
-        -O ${input_bam}.g.vcf \
-        -L ${interval_list} \
-        -ERC GVCF
-    """
-}
-
-/*
- * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls
- */
-process GATK_JOINTGENOTYPING {
-
-    container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"
-
-    publishDir "$params.outdir", mode: 'symlink'
-
-    input:
-        path all_gvcfs
-        path all_idxs
-        path interval_list
-        val cohort_name
-        path ref_fasta
-        path ref_index
-        path ref_dict
-
-    output:
-        path "${cohort_name}.joint.vcf"
-        path "${cohort_name}.joint.vcf.idx"
-
-    script:
-        def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ')
-    """
-    gatk GenomicsDBImport \
-        ${gvcfs_line} \
-        -L ${interval_list} \
-        --genomicsdb-workspace-path ${cohort_name}_gdb
-
-    gatk GenotypeGVCFs \
-        -R ${ref_fasta} \
-        -V gendb://${cohort_name}_gdb \
-        -L ${interval_list} \
-        -O ${cohort_name}.joint.vcf
-    """
-}
-
-/*
- * Generate statistics with bcftools stats
- */
-process BCFTOOLS_STATS {
-
-    container 'community.wave.seqera.io/library/bcftools:1.20--a7f1d9cdda56cc93'
-    conda "bioconda::bcftools=1.20"
-
-    input:
-        path vcf_file
-
-    output:
-        path "${vcf_file}.stats"
-
-    """
-    bcftools stats ${vcf_file} > ${vcf_file}.stats
-    """
-}
-
-/*
- * Generate MultiQC report
- */
-process MULTIQC {
-
-    container 'community.wave.seqera.io/library/multiqc:1.24.1--789bc3917c8666da'
-    conda "bioconda::multiqc=1.24.1"
-
-    publishDir "$params.outdir", mode: 'copy'
-
-    input:
-        path input_files
-        val cohort_name
-
-    output:
-        path "${params.cohort_name}_multiqc_report.html"
-
-    """
-    multiqc \\
-        --force \\
-        -o . \\
-        -n ${cohort_name}_multiqc_report.html \\
-        --clean-up \\
-        ${input_files}
-    """
-}
+// Include modules
+include { SAMTOOLS_INDEX       } from './modules/local/samtools/index/main.nf'
+include { GATK_HAPLOTYPECALLER } from './modules/local/gatk/haplotypecaller/main.nf'
+include { GATK_JOINTGENOTYPING } from './modules/local/gatk/jointgenotyping/main.nf'
+include { BCFTOOLS_STATS       } from './modules/local/bcftools/stats/main.nf'
+include { MULTIQC              } from './modules/local/multiqc/multiqc/main.nf'
 
 workflow {
 
@@ -168,16 +23,16 @@ workflow {
 
     // Call variants from the indexed BAM file
     GATK_HAPLOTYPECALLER(
-        SAMTOOLS_INDEX.out,
+        SAMTOOLS_INDEX.out.bam_bai,
         ref_file,
         ref_index_file,
         ref_dict_file,
         intervals_file
     )
 
     // Collect variant calling outputs across samples
-    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out[0].collect()
-    all_idxs_ch = GATK_HAPLOTYPECALLER.out[1].collect()
+    all_gvcfs_ch = GATK_HAPLOTYPECALLER.out.vcf.collect()
+    all_idxs_ch = GATK_HAPLOTYPECALLER.out.idx.collect()
 
     // Combine GVCFs into a GenomicsDB data store and apply joint genotyping
     GATK_JOINTGENOTYPING(
@@ -191,11 +46,11 @@ workflow {
     )
 
     BCFTOOLS_STATS(
-        GATK_JOINTGENOTYPING.out[0]
+        GATK_JOINTGENOTYPING.out.vcf
     )
 
     MULTIQC(
-        BCFTOOLS_STATS.out.collect(),
+        BCFTOOLS_STATS.out.stats.collect(),
         params.cohort_name
     )
 }
diff --git a/modules/local/bcftools/stats/main.nf b/modules/local/bcftools/stats/main.nf
@@ -0,0 +1,19 @@
+/*
+ * Generate statistics with bcftools stats
+ */
+process BCFTOOLS_STATS {
+
+    container 'community.wave.seqera.io/library/bcftools:1.20--a7f1d9cdda56cc93'
+    conda "bioconda::bcftools=1.20"
+
+    input:
+        path vcf_file
+
+    output:
+        path "${vcf_file}.stats", emit: stats
+
+    script:
+    """
+    bcftools stats ${vcf_file} > ${vcf_file}.stats
+    """
+}
diff --git a/modules/local/gatk/haplotypecaller/main.nf b/modules/local/gatk/haplotypecaller/main.nf
@@ -0,0 +1,33 @@
+#!/usr/bin/env nextflow
+
+/*
+ * Call variants with GATK HaplotypeCaller
+ */
+process GATK_HAPLOTYPECALLER {
+
+    container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"
+    conda "bioconda::gatk4=4.5.0.0"
+
+    publishDir '${params.outdir}', mode: 'symlink'
+
+    input:
+        tuple path(input_bam), path(input_bam_index)
+        path ref_fasta
+        path ref_index
+        path ref_dict
+        path interval_list
+
+    output:
+        path "${input_bam}.g.vcf"     , emit: vcf
+        path "${input_bam}.g.vcf.idx" , emit: idx
+
+    script:
+    """
+    gatk HaplotypeCaller \
+        -R ${ref_fasta} \
+        -I ${input_bam} \
+        -O ${input_bam}.g.vcf \
+        -L ${interval_list} \
+        -ERC GVCF
+    """
+}
diff --git a/modules/local/gatk/jointgenotyping/main.nf b/modules/local/gatk/jointgenotyping/main.nf
@@ -0,0 +1,38 @@
+/*
+ * Combine GVCFs into GenomicsDB datastore and run joint genotyping to produce cohort-level calls
+ */
+process GATK_JOINTGENOTYPING {
+
+    container "community.wave.seqera.io/library/gatk4:4.5.0.0--730ee8817e436867"
+    conda "bioconda::gatk4=4.5.0.0"
+
+    publishDir '${params.outdir}', mode: 'symlink'
+
+    input:
+        path all_gvcfs
+        path all_idxs
+        path interval_list
+        val cohort_name
+        path ref_fasta
+        path ref_index
+        path ref_dict
+
+    output:
+        path "${cohort_name}.joint.vcf"    , emit: vcf
+        path "${cohort_name}.joint.vcf.idx", emit: idx
+
+    script:
+        def gvcfs_line = all_gvcfs.collect { gvcf -> "-V ${gvcf}" }.join(' ')
+    """
+    gatk GenomicsDBImport \
+        ${gvcfs_line} \
+        -L ${interval_list} \
+        --genomicsdb-workspace-path ${cohort_name}_gdb
+
+    gatk GenotypeGVCFs \
+        -R ${ref_fasta} \
+        -V gendb://${cohort_name}_gdb \
+        -L ${interval_list} \
+        -O ${cohort_name}.joint.vcf
+    """
+}
diff --git a/modules/local/multiqc/multiqc/main.nf b/modules/local/multiqc/multiqc/main.nf
@@ -0,0 +1,27 @@
+/*
+ * Generate MultiQC report
+ */
+process MULTIQC {
+
+    container 'community.wave.seqera.io/library/multiqc:1.24.1--789bc3917c8666da'
+    conda "bioconda::multiqc=1.24.1"
+
+    publishDir "$params.outdir", mode: 'copy'
+
+    input:
+        path input_files
+        val cohort_name
+
+    output:
+        path "${cohort_name}_multiqc_report.html", emit: report
+
+    script:
+    """
+    multiqc \\
+        --force \\
+        -o . \\
+        -n ${cohort_name}_multiqc_report.html \\
+        --clean-up \\
+        ${input_files}
+    """
+}
diff --git a/modules/local/samtools/index/main.nf b/modules/local/samtools/index/main.nf
@@ -0,0 +1,21 @@
+/*
+ * Generate BAM index file
+ */
+process SAMTOOLS_INDEX {
+
+    container 'community.wave.seqera.io/library/samtools:1.20--b5dfbd93de237464'
+    conda "bioconda::samtools=1.20"
+
+    publishDir '${params.outdir}', mode: 'symlink'
+
+    input:
+        path input_bam
+
+    output:
+        tuple path(input_bam), path("${input_bam}.bai"), emit: bam_bai
+
+    script:
+    """
+    samtools index '$input_bam'
+    """
+}