update to version 2.0.0

avantonder · Nov 5, 2024 · e053848 · e053848
1 parent 12fdc75
commit e053848
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Showing 3 changed files with 5 additions and 6 deletions.
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -51,7 +51,7 @@ top_modules:
       info: "Estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree."
       extra: "ℹ️: plot title will say Kraken2 due to the first step of bracken producing the same output format as Kraken. Abundance information is currently not supported in MultiQC."
       path_filters:
-        - "*.bracken.kraken2.report.txt"
+        - "*.kraken2.report_bracken.txt"
 
 table_columns_placement:
   FastQC (raw reads):

diff --git a/nextflow.config b/nextflow.config
@@ -30,7 +30,7 @@ params {
   save_merged                = false
   skip_fastp                 = false
   skip_fastqc                = false
-  extra_fastp_args           = null
+  extra_fastp_args           = '--cut_front --cut_tail --trim_poly_x --cut_mean_quality 30 --qualified_quality_phred 30 --unqualified_percent_limit 10 --length_required 50'
 
   // Kraken 2
   skip_kraken2               = false

diff --git a/workflows/bacqc.nf b/workflows/bacqc.nf
@@ -104,8 +104,6 @@ workflow BACQC {
         params.skip_fastp,
         params.skip_fastqc
     )
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.fastqc_raw_zip.collect{it[1]})
-    ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.fastqc_trim_zip.collect{it[1]})
     ch_versions = ch_versions.mix(FASTQ_TRIM_FASTP_FASTQC.out.versions)
     ch_filtered_reads = FASTQ_TRIM_FASTP_FASTQC.out.reads
 
@@ -166,7 +164,6 @@ workflow BACQC {
             )
         ch_kraken2_bracken             = KRAKEN2_KRAKEN2.out.report
         ch_kraken2_krakenparse         = KRAKEN2_KRAKEN2.out.report
-        ch_kraken2_multiqc             = KRAKEN2_KRAKEN2.out.report
         ch_versions                    = ch_versions.mix(KRAKEN2_KRAKEN2.out.versions.first().ifEmpty(null))
         //
         // MODULE: Run bracken
@@ -260,9 +257,11 @@ workflow BACQC {
         )
     )
 
-    //ch_multiqc_files = ch_multiqc_files.mix( FASTQC_FINAL.out.zip.collect{it[1]}.ifEmpty([]) )
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.fastqc_raw_zip.collect{it[1]})
+    ch_multiqc_files = ch_multiqc_files.mix(FASTQ_TRIM_FASTP_FASTQC.out.fastqc_trim_zip.collect{it[1]})
 
     if (!params.skip_kraken2) {
+        ch_multiqc_files = ch_multiqc_files.mix( KRAKEN2_KRAKEN2.out.report.collect{it[1]}.ifEmpty([]) )
         ch_multiqc_files = ch_multiqc_files.mix( BRACKEN_BRACKEN.out.txt.collect{it[1]}.ifEmpty([]) )
     }