Merge pull request #64 from hoelzer/fix/issue55

Fixes a few issues in the ML/issue55 branch

envs/multiqc.yaml

@@ -2,5 +2,6 @@ name: multiqc
 channels:
   - bioconda
 dependencies:
+  - python<3.12.0
   - multiqc=1.12
 

envs/nanoplot.yaml

@@ -4,4 +4,6 @@ channels:
   - conda-forge
 dependencies:
   - nanoplot=1.32.1
-  - seaborn==0.10.1
+  - seaborn==0.10.1
+  - matplotlib<3.6.0
+  - numpy<1.24.0

modules/alignment_processing.nf

@@ -150,7 +150,7 @@ process idxstats_from_bam {
   tuple val(name), val(type), path(bam), path(bai)
 
   output:
-  tuple val(name), val(type), path('*_idxstats.tsv')
+  tuple val(name), val(type), path('*.idxstats.tsv')
 
   script:
   """
@@ -165,13 +165,13 @@ process idxstats_from_bam {
 process flagstats_from_bam {
   label 'minimap2'
 
-  publishDir "${params.output}/minimap2", mode: params.publish_dir_mode, pattern: "${bam.baseName}_flagstats.txt" 
+  publishDir "${params.output}/minimap2", mode: params.publish_dir_mode, pattern: "${bam.baseName}.flagstats.txt"
 
   input:
   tuple val(name), val(type), path(bam), path(bai)
 
   output:
-  tuple val(name), val(type), path('*_flagstats.txt')
+  tuple val(name), val(type), path('*.flagstats.txt')
 
   script:
   """
@@ -195,7 +195,7 @@ process sort_bam {
   script:
   """
   mv ${bam} ${bam}.tmp
-  samtools sort -@ ${task.cpus} ${bam}.tmp > ${bam.baseName}.bam
+  samtools sort -@ ${task.cpus} ${bam}.tmp > ${bam.baseName}.sorted.bam
   """
   stub:
   """
@@ -223,4 +223,4 @@ process index_bam {
   """
   touch ${bam}.bai
   """
-}
+}

modules/utils.nf

@@ -64,7 +64,7 @@ process get_read_names {
 }
 
 process filter_fastq_by_name {
-  label 'basics'
+  label 'minimap2'  // We don't need minimap2 but the container has pigz
 
   if ( params.keep ) {
     publishDir "${params.output}/${params.tool}", mode: params.publish_dir_mode, pattern: "*.gz"