Merge pull request #93 from Daniel-VM/dev

Redirect the module statistics to multiqc
nf-core · Oct 11, 2023 · 368c6cb · 368c6cb
2 parents 29249d2 + 7cd0e63
commit 368c6cb
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,21 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v2.1.1dev nf-core/bacass: "Navy Steel Swordfish" - 2023/10/11
+
+Enhancement of the MultiQC report.
+
+### `Added`
+
+- [#93](https://github.com/nf-core/bacass/pull/93) - Add missing modules output to MultiQC.
+
+  - Fastp
+  - PycoQC
+  - Porechop
+  - Quast
+  - Kraken2
+  - Prokka
+
 ## v2.1.0dev nf-core/bacass: "Navy Steel Swordfish" - 2023/09/11
 
 This version merges the nf-core template update v2.9. It also updates modules or dependencies to make them work with the new template.

diff --git a/modules.json b/modules.json
@@ -92,7 +92,7 @@
                 "nf-core": {
                     "fastq_trim_fastp_fastqc": {
                         "branch": "master",
-                        "git_sha": "dedc0e31087f3306101c38835d051bf49789445a",
+                        "git_sha": "bd448d5c60454640610681515538be3ec66036e4",
                         "installed_by": ["subworkflows"]
                     }
                 }

diff --git a/modules/nf-core/nanoplot/main.nf b/modules/nf-core/nanoplot/main.nf
diff --git a/modules/nf-core/nanoplot/nanoplot.diff b/modules/nf-core/nanoplot/nanoplot.diff
diff --git a/nextflow.config b/nextflow.config
@@ -252,7 +252,7 @@ manifest {
     description     = """Simple bacterial assembly and annotation"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.1.0dev'
+    version         = '2.1.1dev'
     doi             = '10.5281/zenodo.2669428'
 }
 

diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf b/subworkflows/nf-core/fastq_trim_fastp_fastqc/main.nf
diff --git a/workflows/bacass.nf b/workflows/bacass.nf
@@ -149,6 +149,9 @@ workflow BACASS {
         params.skip_fastp,
         params.skip_fastqc
     )
+    ch_fastqc_raw_multiqc   = FASTQ_TRIM_FASTP_FASTQC.out.fastqc_raw_zip
+    ch_fastqc_trim_multiqc  = FASTQ_TRIM_FASTP_FASTQC.out.fastqc_trim_zip
+    ch_trim_json_multiqc    = FASTQ_TRIM_FASTP_FASTQC.out.trim_json
     ch_versions = ch_versions.mix(FASTQ_TRIM_FASTP_FASTQC.out.versions.ifEmpty(null))
 
     //
@@ -157,26 +160,31 @@ workflow BACASS {
     NANOPLOT (
         ch_longreads
     )
+    ch_nanoplot_txt_multiqc = NANOPLOT.out.txt
     ch_versions = ch_versions.mix(NANOPLOT.out.versions.ifEmpty(null))
 
     //
     // MODULE: PYCOQC, quality check for nanopore reads and Quality/Length Plots
     //
     // TODO: Couldn't be tested. No configuration test available (lack of fast5 file or params.skip_pycoqc=false).
+    ch_pycoqc_multiqc = Channel.empty()
     if ( !params.skip_pycoqc ) {
         PYCOQC (
             ch_fast5.dump(tag: 'fast5')
         )
-        versions = ch_versions.mix(PYCOQC.out.versions.ifEmpty(null))
+        ch_pycoqc_multiqc = PYCOQC.out.json
+        ch_versions       = ch_versions.mix(PYCOQC.out.versions.ifEmpty(null))
     }
 
     //
     // MODULE: PORECHOP, quality check for nanopore reads and Quality/Length Plots
     //
+    ch_porechop_log_multiqc = Channel.empty()
     if ( params.assembly_type == 'hybrid' || params.assembly_type == 'long' && !('short' in params.assembly_type) ) {
         PORECHOP_PORECHOP (
             ch_longreads.dump(tag: 'longreads')
         )
+        ch_porechop_log_multiqc = PORECHOP_PORECHOP.out.log
         ch_versions = ch_versions.mix( PORECHOP_PORECHOP.out.versions.ifEmpty(null) )
     }
 
@@ -229,7 +237,6 @@ workflow BACASS {
     //
     // MODULE: Canu, genome assembly, long reads
     //
-
     if ( params.assembler == 'canu' ) {
         CANU (
             ch_for_assembly.map { meta, reads, lr -> tuple( meta, lr ) },
@@ -335,6 +342,8 @@ workflow BACASS {
     //
     // MODULE: Kraken2, QC for sample purity
     //
+    ch_kraken_short_multiqc = Channel.empty()
+    ch_kraken_long_multiqc  = Channel.empty()
     if ( !params.skip_kraken2 ) {
         KRAKEN2_DB_PREPARATION (
             kraken2db
@@ -345,7 +354,9 @@ workflow BACASS {
             false,
             false
         )
+        ch_kraken_short_multiqc = KRAKEN2.out.report
         ch_versions = ch_versions.mix(KRAKEN2.out.versions.ifEmpty(null))
+
         KRAKEN2_LONG (
             ch_for_kraken2_long
                 .map { meta, reads ->
@@ -359,6 +370,7 @@ workflow BACASS {
             false,
             false
         )
+        ch_kraken_long_multiqc = KRAKEN2_LONG.out.report
         ch_versions = ch_versions.mix(KRAKEN2_LONG.out.versions.ifEmpty(null))
     }
 
@@ -375,11 +387,13 @@ workflow BACASS {
         [[:],[]],
         [[:],[]]
     )
-    ch_versions = ch_versions.mix(QUAST.out.versions.ifEmpty(null))
+    ch_quast_multiqc = QUAST.out.tsv
+    ch_versions      = ch_versions.mix(QUAST.out.versions.ifEmpty(null))
 
     //
     // MODULE: PROKKA, gene annotation
     //
+    ch_prokka_multiqc = Channel.empty()
     if ( !params.skip_annotation && params.annotation_tool == 'prokka' ) {
         GUNZIP ( ch_assembly )
         ch_to_prokka    = GUNZIP.out.gunzip
@@ -390,7 +404,8 @@ workflow BACASS {
             [],
             []
         )
-        ch_versions = ch_versions.mix(PROKKA.out.versions.ifEmpty(null))
+        ch_prokka_multiqc   = PROKKA.out.txt.collect()
+        ch_versions         = ch_versions.mix(PROKKA.out.versions.ifEmpty(null))
     }
 
     //
@@ -425,14 +440,22 @@ workflow BACASS {
         ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml'))
         ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml'))
         ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect())
-        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.fastqc_raw_zip.collect{it[1]}.ifEmpty([]))
-        ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.trim_json.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_fastqc_raw_multiqc.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_fastqc_trim_multiqc.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_trim_json_multiqc.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_kraken_short_multiqc.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_kraken_long_multiqc.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_quast_multiqc.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_prokka_multiqc.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_nanoplot_txt_multiqc.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_porechop_log_multiqc.collect{it[1]}.ifEmpty([]))
+        ch_multiqc_files = ch_multiqc_files.mix(ch_pycoqc_multiqc.collect{it[1]}.ifEmpty([]))
 
         MULTIQC (
             ch_multiqc_files.collect(),
-            ch_multiqc_config.toList(),
-            ch_multiqc_custom_config.toList(),
-            ch_multiqc_logo.toList()
+            ch_multiqc_config,
+            ch_multiqc_custom_config.collect().ifEmpty([]),
+            ch_multiqc_logo.collect().ifEmpty([])
         )
         multiqc_report = MULTIQC.out.report.toList()
     }