Subsitute samtools/bam2fq with samtools/fastq

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#271](https://github.com/nf-core/taxprofiler/pull/271/files) Improved standardised table generation documentation nd mOTUs manual database download tutorial (♥ to @prototaxites for reporting, fix by @jfy133)
 - [#269](https://github.com/nf-core/taxprofiler/pull/269/files) Reduced output files in AWS full test output due to very large files
 - [#270](https://github.com/nf-core/taxprofiler/pull/270/files) Fixed warning for host removal index parameter, and improved index checks (♥ to @prototaxites for reporting, fix by @jfy133)
+- [#274](https://github.com/nf-core/taxprofiler/pull/274/files) Substituted the samtools/bam2fq module with samtools/fastq module (fix by @sofstam)
 
 ### `Dependencies`
 

conf/modules.config

@@ -250,12 +250,12 @@ process {
         ext.prefix = { "${meta.id}_${meta.run_accession}.unmapped" }
     }
 
-    withName: SAMTOOLS_BAM2FQ {
+    withName: SAMTOOLS_FASTQ {
         ext.prefix = { "${meta.id}_${meta.run_accession}.unmapped" }
         publishDir = [
-            path: { "${params.outdir}/samtools/bam2fq" },
+            path: { "${params.outdir}/samtools/fastq" },
             mode: params.publish_dir_mode,
-            pattern: '*.fq.gz',
+            pattern: '*.fastq.gz',
             enabled: params.save_hostremoval_unmapped
         ]
     }

docs/output.md

@@ -21,7 +21,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Bowtie2](#bowtie2) - Host removal for Illumina reads
 - [minimap2](#minimap2) - Host removal for Nanopore reads
 - [SAMtools stats](#samtools-stats) - Statistics from host removal
-- [SAMtools bam2fq](#samtools-bam2fq) - Converts unmapped BAM file to fastq format (minimap2 only)
+- [SAMtools fastq](#samtools-fastq) - Converts unmapped BAM file to fastq format (minimap2 only)
 - [Bracken](#bracken) - Taxonomic classifier using k-mers and abundance estimations
 - [Kraken2](#kraken2) - Taxonomic classifier using exact k-mer matches
 - [KrakenUniq](#krakenuniq) - Taxonomic classifier that combines the k-mer-based classification and the number of unique k-mers found in each species
@@ -201,7 +201,7 @@ It is used with nf-core/taxprofiler to allow removal of 'host' (e.g. human) and/
 
 By default nf-core/taxprofiler will only provide the `.log` file if host removal is turned on. You will only have a `.bam` file if you specify `--save_hostremoval_bam`. This will contain _both_ mapped and unmapped reads. You will only get FASTQ files if you specify to save `--save_hostremoval_unmapped` - these contain only unmapped reads.
 
-> ℹ️ Unmapped reads in FASTQ are only found in this directory for short-reads, for long-reads see [`samtools/bam2fq/`](#samtools-bam2fq)
+> ℹ️ Unmapped reads in FASTQ are only found in this directory for short-reads, for long-reads see [`samtools/fastq/`](#samtools-fastq)
 
 > ⚠️ The resulting `.fastq` files may _not_ always be the 'final' reads that go into taxprofiling, if you also run other steps such as run merging etc..
 
@@ -228,11 +228,11 @@ By default, nf-core/taxprofiler will only provide the `.bam` file containing map
 
 > ℹ️ minimap2 is not yet supported as a module in MultiQC and therefore there is no dedicated section in the MultiQC HTML. Rather, alignment statistics to host genome is reported via samtools stats module in MultiQC report.
 
-> ℹ️ Unlike Bowtie2, minimap2 does not produce an unmapped FASTQ file by itself. See [`samtools/bam2fq`](#samtools-bam2fq)
+> ℹ️ Unlike Bowtie2, minimap2 does not produce an unmapped FASTQ file by itself. See [`samtools/fastq`](#samtools-fastq)
 
-### SAMtools bam2fq
+### SAMtools fastq
 
-[SAMtools bam2fq](http://www.htslib.org/doc/1.1/samtools.html) converts a `.sam`, `.bam`, or `.cram` alignment file to FASTQ format
+[SAMtools fastq](http://www.htslib.org/doc/1.1/samtools.html) converts a `.sam`, `.bam`, or `.cram` alignment file to FASTQ format
 
 <details markdown="1">
 <summary>Output files</summary>

modules.json

@@ -187,9 +187,9 @@
                         "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
                         "installed_by": ["modules"]
                     },
-                    "samtools/bam2fq": {
+                    "samtools/fastq": {
                         "branch": "master",
-                        "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c",
+                        "git_sha": "0f8a77ff00e65eaeebc509b8156eaa983192474b",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {

nextflow_schema.json

@@ -304,7 +304,7 @@
                     "type": "boolean",
                     "fa_icon": "fas fa-save",
                     "description": "Save reads from samples that went through the host-removal step",
-                    "help_text": "Save only the reads NOT mapped to the reference genome in FASTQ format (as exported from `samtools view` and `bam2fq`).\n\nThis can be useful if you wish to perform other analyses on the off-target reads from the host mapping, such as manual profiling or _de novo_ assembly."
+                    "help_text": "Save only the reads NOT mapped to the reference genome in FASTQ format (as exported from `samtools view` and `fastq`).\n\nThis can be useful if you wish to perform other analyses on the off-target reads from the host mapping, such as manual profiling or _de novo_ assembly."
                 }
             },
             "fa_icon": "fas fa-user-times"

subworkflows/local/longread_hostremoval.nf

@@ -5,7 +5,7 @@
 include { MINIMAP2_INDEX             } from '../../modules/nf-core/minimap2/index/main'
 include { MINIMAP2_ALIGN             } from '../../modules/nf-core/minimap2/align/main'
 include { SAMTOOLS_VIEW              } from '../../modules/nf-core/samtools/view/main'
-include { SAMTOOLS_BAM2FQ            } from '../../modules/nf-core/samtools/bam2fq/main'
+include { SAMTOOLS_FASTQ             } from '../../modules/nf-core/samtools/fastq/main'
 include { SAMTOOLS_INDEX             } from '../../modules/nf-core/samtools/index/main'
 include { SAMTOOLS_STATS             } from '../../modules/nf-core/samtools/stats/main'
 
@@ -38,8 +38,8 @@ workflow LONGREAD_HOSTREMOVAL {
     SAMTOOLS_VIEW ( ch_minimap2_mapped , [], [] )
     ch_versions      = ch_versions.mix( SAMTOOLS_VIEW.out.versions.first() )
 
-    SAMTOOLS_BAM2FQ ( SAMTOOLS_VIEW.out.bam, false )
-    ch_versions      = ch_versions.mix( SAMTOOLS_BAM2FQ.out.versions.first() )
+    SAMTOOLS_FASTQ ( SAMTOOLS_VIEW.out.bam, false )
+    ch_versions      = ch_versions.mix( SAMTOOLS_FASTQ.out.versions.first() )
 
     // Indexing whole BAM for host removal statistics
     SAMTOOLS_INDEX ( MINIMAP2_ALIGN.out.bam )
@@ -54,7 +54,7 @@ workflow LONGREAD_HOSTREMOVAL {
 
     emit:
     stats    = SAMTOOLS_STATS.out.stats     //channel: [val(meta), [reads  ] ]
-    reads    = SAMTOOLS_BAM2FQ.out.reads   // channel: [ val(meta), [ reads ] ]
+    reads    = SAMTOOLS_FASTQ.out.fastq.mix( SAMTOOLS_FASTQ.out.other)   // channel: [ val(meta), [ reads ] ]
     versions = ch_versions                 // channel: [ versions.yml ]
     mqc      = ch_multiqc_files
 }