kfukuta/wf-transcriptomes-v202
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Merge branch 'pychopper_report_move' into 'dev'

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Move pychopper report up to qc section

See merge request epi2melabs/workflow-containers/wf-transcriptomes!69
This commit is contained in:
Neil Horner 2022-08-04 15:46:56 +00:00
commit fad574dacf
1 changed files with 5 additions and 5 deletions
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bin/report.py
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@ -882,7 +882,7 @@ def main():
"Transcript isoform report", "wf-transcriptomes", "Transcript isoform report", "wf-transcriptomes",
revision=args.revision, commit=args.commit) revision=args.revision, commit=args.commit)
# Add reads summary section # QC
seq_stats_tabs(report, args.sample_ids, args.summaries) seq_stats_tabs(report, args.sample_ids, args.summaries)
if args.alignment_stats is not None: if args.alignment_stats is not None:
@ -897,7 +897,10 @@ def main():
section.table(df_aln_stats) section.table(df_aln_stats)
# workflow-specific plotting if args.pychop_report is not None:
pychopper_plots(report, args.pychop_report)
# Results
transcriptome_summary( transcriptome_summary(
report, args.gff_annotation, sample_ids, denovo=args.denovo) report, args.gff_annotation, sample_ids, denovo=args.denovo)
@ -908,9 +911,6 @@ def main():
report.write(args.report) report.write(args.report)
if args.pychop_report is not None:
pychopper_plots(report, args.pychop_report)
if df_tmaps is not None: if df_tmaps is not None:
transcript_table(report, df_tmaps, args.transcript_table_cov_thresh) transcript_table(report, df_tmaps, args.transcript_table_cov_thresh)