Merge branch 'inline-barcode-trimming' of github.com:nf-core/eager into inline-barcode-trimming

Author: jfy133

.github/workflows/ci.yml

@@ -59,7 +59,7 @@ jobs:
           git clone --single-branch --branch eager https://github.com/nf-core/test-datasets.git data
       - name: DELAY to try address some odd behaviour with what appears to be a conflict between parallel htslib jobs leading to CI hangs
         run: | 
-          if [[ $NXF_VER = '' ]]; then sleep 360; fi
+          if [[ $NXF_VER = '' ]]; then sleep 1200; fi
       - name: BASIC Run the basic pipeline with directly supplied single-end FASTQ
         run: |
           nextflow run ${GITHUB_WORKSPACE} -profile test,docker --input 'data/testdata/Mammoth/fastq/*_R1_*.fq.gz' --single_end
@@ -200,4 +200,4 @@ jobs:
           nextflow run ${GITHUB_WORKSPACE} -profile test_tsv_humanbam,docker --skip_fastqc --skip_adapterremoval --skip_deduplication --skip_qualimap --skip_preseq --skip_damage_calculation --run_mtnucratio
       - name: RESCALING Run basic pipeline with basic pipeline but with mapDamage rescaling of BAM files. Note this will be slow
         run: |
-          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'
+          nextflow run ${GITHUB_WORKSPACE} -profile test_tsv,docker --run_mapdamage_rescaling --run_genotyping --genotyping_tool hc --genotyping_source 'rescaled'