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>

modules/fgbio/fastqtobam/main.nf

@@ -9,10 +9,10 @@ process FGBIO_FASTQTOBAM {
 
     input:
     tuple val(meta), path(reads)
-    val read_structure
 
     output:
-    tuple val(meta), path("*_umi_converted.bam"), emit: umibam
+    tuple val(meta), path("*.bam") , emit: bam , optional: true
+    tuple val(meta), path("*.cram"), emit: cram, optional: true
     path "versions.yml"            , emit: versions
 
     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}":

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"

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 )
 }

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"
+    }
 }

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/fastqtobam
     - fgbio
+    - fgbio/fastqtobam
   files:
-    - path: output/fgbio/test_umi_converted.bam
+    - 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.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