Merge pull request #536 from nf-core/final_review

Overwrite the search patten of filtlong in multiqc_config.yml
nf-core · Oct 1, 2024 · 7e4734a · 7e4734a
2 parents 7d7d0c7 + 60dc5a0
commit 7e4734a
Show file tree

Hide file tree

Showing 18 changed files with 25 additions and 35 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -21,6 +21,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#531](https://github.com/nf-core/taxprofiler/pull/531) Fix FASTA input validation in schema allowing FASTQ extension, expand allowed FASTA extensions (fixed by @jfy133)
 - [#512](https://github.com/nf-core/taxprofiler/pull/532) Minor formatting and ordering improvements in MultiQC report (by @jfy133)
 - [#532](https://github.com/nf-core/taxprofiler/pull/532) - Added missing documentation behind the 'ignore' BRACKEN_BRACKEN error strategy (❤️ to @Mavti for reporting, fixed by @jfy133)
+- [#536](https://github.com/nf-core/taxprofiler/pull/536) - Redefine `contents_re` for filtlong to fix its missing from the MultiQC report (fixed by @LilyAnderssonLee)
 
 ### `Dependencies`
 

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -89,6 +89,9 @@ sp:
     fn: "*_fastqc.zip"
   nonpareil:
     fn: "nonpareil_all_samples.json"
+  filtlong:
+    contents: Scoring long reads
+    contents_re: " "
 
 top_modules:
   - "fastqc":

diff --git a/conf/test_alternativepreprocessing.config b/conf/test_alternativepreprocessing.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_alternativepreprocessing,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_bbduk.config b/conf/test_bbduk.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_bbduk,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_falco.config b/conf/test_falco.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_falco,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_fastp.config b/conf/test_fastp.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_fastp,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_krakenuniq.config b/conf/test_krakenuniq.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_krakenuniq,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_malt.config b/conf/test_malt.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_malt,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -32,7 +32,7 @@ params {
     perform_shortread_complexityfilter     = false
     perform_shortread_hostremoval          = false
     perform_longread_hostremoval           = false
-    perform_runmerging                     = false
+    perform_runmerging                     = true
     hostremoval_reference                  = params.pipelines_testdata_base_path + 'modules/data/genomics/homo_sapiens/genome/genome.fasta'
     run_kaiju                              = false
     run_kraken2                            = false

diff --git a/conf/test_motus.config b/conf/test_motus.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_motus,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_nopreprocessing.config b/conf/test_nopreprocessing.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_nopreprocessing,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_noprofiling.config b/conf/test_noprofiling.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_noprofiling,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */
@@ -48,7 +48,6 @@ process {
     withName: MALT_RUN {
         maxForks = 1
     }
-
     withName: NONPAREIL_NONPAREIL {
         ext.args = { "-k 5" }
     }

diff --git a/conf/test_nothing.config b/conf/test_nothing.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_nothing,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/conf/test_prinseqplusplus.config b/conf/test_prinseqplusplus.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/taxprofiler -profile test,<docker/singularity> --outdir <OUTDIR>
+        nextflow run nf-core/taxprofiler -profile test_prinseqplusplus,<docker/singularity> --outdir <OUTDIR>
 
 ----------------------------------------------------------------------------------------
 */

diff --git a/docs/output.md b/docs/output.md
@@ -730,14 +730,6 @@ The 'General Stats' table by default will only show statistics referring to pre-
 For example, DIAMOND output does not have a dedicated section in the MultiQC HTML, only in the general stats table. To turn this on, copy the nf-core/taxprofiler [MultiQC config](https://github.com/nf-core/taxprofiler/blob/master/assets/multiqc_config.yml) and change the DIAMOND entry in `table_columns_visible:` to True.
 :::
 
-:::info
-In the 'General Stats' table, files that end with `_R1/_R2` or `_1/_2` prior the file format extension will be collapsed into single rows.
-
-It is assumed that file names only differening by these characters are associated paired-end reads and stats should be reported together.
-
-For example `sample1_R1.fastq.gz` and `sample1_R2.fastq.gz` will be reported together as `sample1`, with R1/R2 specific stats included inside the collapsed row.
-:::
-
 ### Pipeline information
 
 <details markdown="1">

diff --git a/docs/usage.md b/docs/usage.md
@@ -101,11 +101,6 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p
 FASTA input will not go through any preprocessing steps, and will go directly to profiling.
 :::
 
-:::warning
-Files names prior the file format extension that include `_R1`/`_R2`, or `_1`/`_2` will be automatically be collapsed in the MultiQC report's General Stats table.
-Please see output documentation for more information.
-:::
-
 ### Full database sheet
 
 nf-core/taxprofiler supports multiple databases being classified/profiled against in parallel for each tool.

diff --git a/subworkflows/local/longread_adapterremoval.nf b/subworkflows/local/longread_adapterremoval.nf
@@ -1,5 +1,5 @@
 //
-// Process long raw reads with porechop
+// Process long raw reads with porechop or porechop_abi
 //
 
 include { PORECHOP_PORECHOP          } from '../../modules/nf-core/porechop/porechop/main'
@@ -13,17 +13,17 @@ workflow LONGREAD_ADAPTERREMOVAL {
     ch_versions      = Channel.empty()
     ch_multiqc_files = Channel.empty()
 
-    if (params.longread_adapterremoval_tool == 'porechop_abi') {
-        PORECHOP_ABI (reads)
+    if ( params.longread_adapterremoval_tool == 'porechop_abi' ) {
+        PORECHOP_ABI ( reads )
         ch_processed_reads = PORECHOP_ABI.out.reads
             .map { meta, reads -> [meta + [ single_end: true ], reads ] }
         ch_versions = ch_versions.mix( PORECHOP_ABI.out.versions.first() )
         ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_ABI.out.log )
-    } else if (params.longread_adapterremoval_tool == 'porechop') {
+    } else if ( params.longread_adapterremoval_tool == 'porechop' ) {
         PORECHOP_PORECHOP ( reads )
         ch_processed_reads = PORECHOP_PORECHOP.out.reads
-            .map { meta, reads -> [ meta + [single_end: true], reads ] }
-        ch_versions = ch_versions.mix(PORECHOP_PORECHOP.out.versions.first())
+            .map { meta, reads -> [ meta + [ single_end: true ], reads ] }
+        ch_versions = ch_versions.mix( PORECHOP_PORECHOP.out.versions.first() )
         ch_multiqc_files = ch_multiqc_files.mix( PORECHOP_PORECHOP.out.log )
     } else {
         ch_processed_reads = reads

diff --git a/subworkflows/local/longread_filtering.nf b/subworkflows/local/longread_filtering.nf
@@ -1,5 +1,5 @@
 //
-// Check input samplesheet and get read channels
+// Perform filtering
 //
 
 include { FILTLONG                   } from '../../modules/nf-core/filtlong/main'

diff --git a/subworkflows/local/profiling.nf b/subworkflows/local/profiling.nf
@@ -74,9 +74,9 @@ workflow PROFILING {
 
     // Join short and long reads with their corresponding short/long database
     // Note that for not-specified `short;long`, it will match with the database.
-    // E.g. if there is no 'long' reads the above generted 'long' database channel element
+    // E.g. if there is no 'long' reads the above generated 'long' database channel element
     //  will have nothing to join to and will be discarded
-    // Final output: [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':1], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'mal95', 'db_params':'"-id 90"'], <db_path>/malt90]
+    // Final output [DUMP: reads_plus_db] [['id':'2612', 'run_accession':'combined', 'instrument_platform':'ILLUMINA', 'single_end':false, 'is_fasta':false, 'type':'short'], <reads_path>/2612.merged.fastq.gz, ['tool':'malt', 'db_name':'malt95', 'db_params':'"-id 90"', 'type':'short'], <db_path>/malt95]
 
     ch_input_for_profiling = reads
         .map{