Remove unused CI parameter and add additional qualimap column to GeneralStats

Author: jfy133

.github/workflows/ci.yml

@@ -67,7 +67,7 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --bwa_index 'results/reference_genome/bwa_index/BWAIndex/Mammoth_MT_Krause.fasta' --fasta_index 'https://github.com/nf-core/test-datasets/blob/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.fai' 
       - name: REFERENCE Run the basic pipeline with FastA reference with `fna` extension
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker ${{ matrix.endedness }}
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_fna,docker
       - name: REFERENCE Test with zipped reference input
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --fasta 'https://github.com/nf-core/test-datasets/raw/eager/reference/Mammoth/Mammoth_MT_Krause.fasta.gz'

assets/multiqc_config.yaml

@@ -156,6 +156,7 @@ table_columns_visible:
     mtnucratio: 
         mt_nuc_ratio: True
     QualiMap:
+        mapped_reads: True
         mean_coverage: True
         1_x_pc: True
         5_x_pc: True
@@ -235,7 +236,8 @@ table_columns_placement:
         mt_cov_avg: 770
         mt_nuc_ratio: 780
     QualiMap:
-        mean_coverage: 800
+        mapped_reads: 800
+        mean_coverage: 805
         median_coverage: 810
         1_x_pc: 820
         2_x_pc: 830

main.nf

@@ -1884,7 +1884,6 @@ process endorSpy {
     tuple samplename, libraryid, lane, seqtype, organism, strandedness, udg, file("*.json") into ch_endorspy_for_multiqc
 
     script:
-
     if (params.run_bam_filtering) {
       """
       endorS.py -o json -n ${libraryid} ${stats} ${poststats}