nf-core · skrakau · Jun 13, 2022 · Jun 3, 2022 · Jun 8, 2022 · Jun 8, 2022
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,9 +27,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#305](https://github.com/nf-core/mag/pull/305) - Add missing Bowtie2 version for process `BOWTIE2_PHIX_REMOVAL_ALIGN` to `software_versions.yml`
 - [#307](https://github.com/nf-core/mag/pull/307) - Fix retrieval of GTDB-Tk version (note about newer version caused error in `CUSTOM_DUMPSOFTWAREVERSIONS`)
 - [#309](https://github.com/nf-core/mag/pull/309) - Fix publishing of BUSCO `busco_downloads/` folder, i.e. publish only when `--save_busco_reference` is specified
+- [#321](https://github.com/nf-core/mag/pull/321) - Fix parameter processing in `BOWTIE2_REMOVAL_ALIGN` (which was erroneously for `BOWTIE2_PHIX_REMOVAL_ALIGN`)
 
 ### `Dependencies`
 
+| Tool    | Previous version | New version |
+| ------- | ---------------- | ----------- |
+| fastp   | 0.20.1           | 0.23.2      |
+| MultiQC | 1.11             | 1.12        |
+
 ## v2.1.1 - 2021/11/25
 
 ### `Added`

diff --git a/conf/modules.config b/conf/modules.config
@@ -75,7 +75,7 @@ process {
     }
 
     withName: BOWTIE2_PHIX_REMOVAL_ALIGN {
-        ext.suffix = "phix_removed"
+        ext.prefix = { "${meta.id}.phix_removed" }
         publishDir = [
             path: { "${params.outdir}/QC_shortreads/remove_phix" },
             mode: params.publish_dir_mode,
@@ -84,7 +84,9 @@ process {
     }
 
     withName: BOWTIE2_HOST_REMOVAL_ALIGN {
-        ext.suffix = "host_removed"
+        ext.args = params.host_removal_verysensitive ? "--very-sensitive" : "--sensitive"
+        ext.args2 = params.host_removal_save_ids ? "--host_removal_save_ids" : ''
+        ext.prefix = { "${meta.id}.host_removed" }
         publishDir = [
             path: { "${params.outdir}/QC_shortreads/remove_host" },
             mode: params.publish_dir_mode,
@@ -111,7 +113,7 @@ process {
     }
 
     withName: NANOPLOT_RAW {
-        ext.suffix = 'raw'
+        ext.prefix = 'raw'
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,
@@ -120,7 +122,7 @@ process {
     }
 
     withName: NANOPLOT_FILTERED {
-        ext.suffix = 'filtered'
+        ext.prefix = 'filtered'
         publishDir = [
             path: { "${params.outdir}/QC_longreads/NanoPlot/${meta.id}" },
             mode: params.publish_dir_mode,

diff --git a/conf/test_adapterremoval.config b/conf/test_adapterremoval.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/mag -profile test,<docker/singularity>
+        nextflow run nf-core/mag -profile test,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_ancient_dna.config b/conf/test_ancient_dna.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/mag -profile test_ancient_dna,<docker/singularity>
+        nextflow run nf-core/mag -profile test_ancient_dna,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_busco_auto.config b/conf/test_busco_auto.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/mag -profile test_busco_auto,<docker/singularity>
+        nextflow run nf-core/mag -profile test_busco_auto,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_host_rm.config b/conf/test_host_rm.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/mag -profile test_host_rm,<docker/singularity>
+        nextflow run nf-core/mag -profile test_host_rm,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_hybrid.config b/conf/test_hybrid.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/mag -profile test_hybrid,<docker/singularity>
+        nextflow run nf-core/mag -profile test_hybrid,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_hybrid_host_rm.config b/conf/test_hybrid_host_rm.config
@@ -5,7 +5,7 @@
     Defines input files and everything required to run a fast and simple pipeline test.
 
     Use as follows:
-        nextflow run nf-core/mag -profile test_hybrid_host_rm,<docker/singularity>
+        nextflow run nf-core/mag -profile test_hybrid_host_rm,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/docs/output.md b/docs/output.md
@@ -18,6 +18,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 - [Taxonomic classification of binned genomes](#taxonomic-classification-of-binned-genomes)
 - [Genome annotation of binned genomes](#genome-annotation-of-binned-genomes)
 - [Additional summary for binned genomes](#additional-summary-for-binned-genomes)
+- [Ancient DNA](#ancient-dna)
 - [MultiQC](#multiqc) - aggregate report, describing results of the whole pipeline
 - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution
 
@@ -89,7 +90,8 @@ The pipeline uses bowtie2 to map short reads against the host reference genome s
 <summary>Output files</summary>
 
 - `QC_shortreads/remove_host/`
-  - `[sample].host_removed.bowtie2.log`: Contains the bowtie2 log file indicating how many reads have been mapped as well as a file listing the read ids of discarded reads.
+  - `[sample].host_removed.bowtie2.log`: Contains the bowtie2 log file indicating how many reads have been mapped.
+  - `[sample].host_removed.mapped*.read_ids.txt`: Contains a file listing the read ids of discarded reads.
 
 </details>
 
@@ -511,7 +513,9 @@ Whole genome annotation is the process of identifying features of interest in a
 
 </details>
 
-## Ancient DNA (optional, only with `-profile ancient_dna`)
+## Ancient DNA
+
+Optional, only running when parameter `-profile ancient_dna` is specified.
 
 ### `PyDamage`
 

diff --git a/modules/local/bowtie2_removal_align.nf b/modules/local/bowtie2_removal_align.nf
@@ -2,7 +2,7 @@
  * Bowtie2 for read removal
  */
 process BOWTIE2_REMOVAL_ALIGN {
-    tag "${meta.id}-${task.ext.suffix}"
+    tag "$meta.id"
 
     conda (params.enable_conda ? "bioconda::bowtie2=2.4.2" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -21,15 +21,15 @@ process BOWTIE2_REMOVAL_ALIGN {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix    = task.ext.suffix ? "${meta.id}.${task.ext.suffix}" : "${meta.id}"
-    def sensitivity = params.host_removal_verysensitive ? "--very-sensitive" : "--sensitive"
-    def save_ids = params.host_removal_save_ids ? "Y" : "N"
+    def args2 = task.ext.args2 ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def save_ids = (args2.contains('--host_removal_save_ids')) ? "Y" : "N"
     if (!meta.single_end){
         """
         bowtie2 -p ${task.cpus} \
                 -x ${index[0].getSimpleName()} \
                 -1 "${reads[0]}" -2 "${reads[1]}" \
-                $sensitivity \
+                $args \
                 --un-conc-gz ${prefix}.unmapped_%.fastq.gz \
                 --al-conc-gz ${prefix}.mapped_%.fastq.gz \
                 1> /dev/null \
@@ -50,7 +50,7 @@ process BOWTIE2_REMOVAL_ALIGN {
         bowtie2 -p ${task.cpus} \
                 -x ${index[0].getSimpleName()} \
                 -U ${reads} \
-                $sensitivity \
+                $args \
                 --un-gz ${prefix}.unmapped.fastq.gz \
                 --al-gz ${prefix}.mapped.fastq.gz \
                 1> /dev/null \

diff --git a/modules/local/nanoplot.nf b/modules/local/nanoplot.nf
@@ -16,8 +16,8 @@ process NANOPLOT {
     path "versions.yml" , emit: versions
 
     script:
-    def prefix = task.ext.suffix ? "-p ${task.ext.suffix}_" : ''
-    def title  = task.ext.suffix ? "${meta.id}_${task.ext.suffix}" : "${meta.id}"
+    def prefix = task.ext.prefix ? "-p ${task.ext.prefix}_" : ''
+    def title  = task.ext.prefix ? "${meta.id}_${task.ext.prefix}" : "${meta.id}"
     """
     NanoPlot -t ${task.cpus} \
             ${prefix} \