Fgbio/fastqtobam (#1980)

* fix samtools stats thread usage * fix samtools stats thread usage (#1975) * fix samtools stats thread usage * fix checksums * Fix/samtools flagstat (#1979) * fix samtools stats thread usage * flagstat: fix threads * Update busco to v5.4.3 and tar small files (#1970) * Update busco to v5.4.3 and tar small files * Fix file contain strings * Swap md5sums to contains for variable files * Simplify and generalize module * add test.yml * Update modules/fgbio/fastqtobam/meta.yml Co-authored-by: Moritz E. Beber <midnighter@posteo.net> * add support + tests for cram output * more tweaks * update test.yml * prettier * try to fix tests * fix tests * prettier * drop checksum for cram Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Moritz E. Beber <midnighter@posteo.net>
2 years ago · 36049bf544
parent 09acfad211
commit 36049bf544
5 changed files with 145 additions and 28 deletions
--- a/modules/fgbio/fastqtobam/main.nf
+++ b/modules/fgbio/fastqtobam/main.nf
@ -9,11 +9,11 @@ process FGBIO_FASTQTOBAM {

    input:
    tuple val(meta), path(reads)
-    val read_structure

    output:
-    tuple val(meta), path("*_umi_converted.bam"), emit: umibam
-    path "versions.yml"                         , emit: versions
+    tuple val(meta), path("*.bam") , emit: bam , optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
+    path "versions.yml"            , emit: versions

    when:
    task.ext.when == null || task.ext.when
@ -21,17 +21,19 @@ process FGBIO_FASTQTOBAM {
    script:
    def args = task.ext.args ?: ''
    def prefix = task.ext.prefix ?: "${meta.id}"
+    def sample_name = args.contains("--sample") ? "" : "--sample ${prefix}"
+    def library_name = args.contains("--library") ? "" : "--library ${prefix}"
+    def output = prefix =~ /\.(bam|cram)$/ ? prefix : "${prefix}.bam"
    """

    fgbio \\
        --tmp-dir=. \\
        FastqToBam \\
-        -i $reads \\
-        -o "${prefix}_umi_converted.bam" \\
-        --read-structures $read_structure \\
-        --sample $meta.id \\
-        --library $meta.id \\
-        $args
+        ${args} \\
+        --input ${reads} \\
+        --output ${output} \\
+        ${sample_name} \\
+        ${library_name}

    cat <<-END_VERSIONS > versions.yml
    "${task.process}":
--- a/modules/fgbio/fastqtobam/meta.yml
+++ b/modules/fgbio/fastqtobam/meta.yml
@ -1,6 +1,6 @@
 name: fgbio_fastqtobam
 description: |
-  Using the FGBIO tools, converts FASTQ files sequenced with UMIs into BAM files, moving the UMI barcode into the RX field of the BAM file
+  Using the fgbio tools, converts FASTQ files sequenced into unaligned BAM or CRAM files possibly moving the UMI barcode into the RX field of the reads
 keywords:
  - fastqtobam
  - fgbio
@ -19,15 +19,6 @@ input:
      description: pair of reads to be converted into BAM file
      pattern: "*.{fastq.gz}"

-  - read_structure:
-      type: string
-      description: |
-        A read structure should always be provided for each of the fastq files.
-        If single end, the string will contain only one structure (i.e. "2M11S+T"), if paired-end the string
-        will contain two structures separated by a blank space (i.e. "2M11S+T 2M11S+T").
-        If the read does not contain any UMI, the structure will be +T (i.e. only template of any length).
-        https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures
-
 output:
  - meta:
      type: map
@ -38,10 +29,15 @@ output:
      type: file
      description: File containing software version
      pattern: "*.{version.yml}"
-  - umibam:
+  - bam:
      type: file
-      description: Converted, unsorted BAM file with RX tag reporting UMI sequence (if any)
+      description: Unaligned, unsorted BAM file
      pattern: "*.{bam}"
+  - cram:
+      type: file
+      description: Unaligned, unsorted CRAM file
+      pattern: "*.{cram}"

 authors:
  - "@lescai"
+  - "@matthdsm"
--- a/tests/modules/fgbio/fastqtobam/main.nf
+++ b/tests/modules/fgbio/fastqtobam/main.nf
@ -4,7 +4,7 @@ nextflow.enable.dsl = 2

 include { FGBIO_FASTQTOBAM } from '../../../../modules/fgbio/fastqtobam/main.nf'

-workflow test_fgbio_fastqtobam {
+workflow test_fgbio_fastqtobam_paired_default {

    input = [
        [ id:'test', single_end:false ], // meta map
@ -13,7 +13,71 @@ workflow test_fgbio_fastqtobam {
            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
        ]
    ]
-    read_structure = "+T 12M11S+T"

-    FGBIO_FASTQTOBAM ( input, read_structure )
+    FGBIO_FASTQTOBAM ( input )
+}
+
+
+workflow test_fgbio_fastqtobam_paired_cram {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
+
+workflow test_fgbio_fastqtobam_paired_bam {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
+
+workflow test_fgbio_fastqtobam_single {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
+
+workflow test_fgbio_fastqtobam_paired_umi {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
+}
+
+workflow test_fgbio_fastqtobam_paired_custom_samplename {
+
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        [
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
+            file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true)
+        ]
+    ]
+
+    FGBIO_FASTQTOBAM ( input )
 }
--- a/tests/modules/fgbio/fastqtobam/nextflow.config
+++ b/tests/modules/fgbio/fastqtobam/nextflow.config
@ -1,5 +1,16 @@
 process {

    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-
+    withName: "test_fgbio_fastqtobam_paired_cram:FGBIO_FASTQTOBAM" {
+        ext.prefix = {"${meta.id}.cram"}
+    }
+    withName: "test_fgbio_fastqtobam_paired_bam:FGBIO_FASTQTOBAM" {
+        ext.prefix = {"${meta.id}.bam"}
+    }
+    withName: "test_fgbio_fastqtobam_paired_umi:FGBIO_FASTQTOBAM" {
+        ext.args = "--read-structures +T 12M11S+T"
+    }
+    withName: "test_fgbio_fastqtobam_paired_custom_samplename:FGBIO_FASTQTOBAM" {
+        ext.args = "--sample CustomSample --library CustomLibrary"
+    }
 }
--- a/tests/modules/fgbio/fastqtobam/test.yml
+++ b/tests/modules/fgbio/fastqtobam/test.yml
@ -1,8 +1,52 @@
- name: fgbio fastqtobam test_fgbio_fastqtobam
-  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam -c ./tests/config/nextflow.config -c ./tests/modules/fgbio/fastqtobam/nextflow.config
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_default
+  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_default -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: 83cd60e01e5ab90ea3729431ce401add
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_cram
+  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_cram -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.cram
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_bam
+  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_bam -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: 83f879e3a302ca8a50dc9675be7a9216
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_single
+  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_single -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: c08fe1b035b972808f05128e37e8e669
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_umi
+  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_umi -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
+  tags:
    - fgbio
+    - fgbio/fastqtobam
  files:
-    - path: output/fgbio/test_umi_converted.bam
+    - path: output/fgbio/test.bam
      md5sum: 9510735554e5eff29244077a72075fb6
+
+- name: fgbio fastqtobam test_fgbio_fastqtobam_paired_custom_samplename
+  command: nextflow run ./tests/modules/fgbio/fastqtobam -entry test_fgbio_fastqtobam_paired_custom_samplename -c ./tests/config/nextflow.config  -c ./tests/modules/fgbio/fastqtobam/nextflow.config
+  tags:
+    - fgbio
+    - fgbio/fastqtobam
+  files:
+    - path: output/fgbio/test.bam
+      md5sum: ab8d7d2d9c1559b19a501d120296ebe0