Mercurial > repos > public-health-bioinformatics > fastp_json_to_tabular
changeset 4:b86961fa4ac4 draft default tip
"planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/tree/master/tools/fastp_json_to_tabular commit 0cedf8014d943912974969f1ed294f6d0ec8f258"
| author | public-health-bioinformatics |
|---|---|
| date | Thu, 10 Mar 2022 19:14:05 +0000 |
| parents | e342bf27e717 |
| children | |
| files | fastp_json_to_tabular.py test-data/test-02_fastp.tsv |
| diffstat | 2 files changed, 3 insertions(+), 3 deletions(-) [+] |
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--- a/fastp_json_to_tabular.py Thu Mar 10 19:03:59 2022 +0000 +++ b/fastp_json_to_tabular.py Thu Mar 10 19:14:05 2022 +0000 @@ -10,8 +10,8 @@ reads_single_paired = fastp_report['summary']['sequencing'].split(' ')[0] if reads_single_paired == 'paired': - total_read_pairs_before_filtering = str(int(fastp_report['summary']['before_filtering']['total_reads']) / 2) - total_read_pairs_after_filtering = str(int(fastp_report['summary']['after_filtering']['total_reads']) / 2) + total_read_pairs_before_filtering = str(int(int(fastp_report['summary']['before_filtering']['total_reads']) / 2)) + total_read_pairs_after_filtering = str(int(int(fastp_report['summary']['after_filtering']['total_reads']) / 2)) read2_mean_length_before_filtering = fastp_report['summary']['before_filtering']['read2_mean_length'] read2_mean_length_after_filtering = fastp_report['summary']['after_filtering']['read2_mean_length'] else:
--- a/test-data/test-02_fastp.tsv Thu Mar 10 19:03:59 2022 +0000 +++ b/test-data/test-02_fastp.tsv Thu Mar 10 19:14:05 2022 +0000 @@ -1,2 +1,2 @@ total_reads_before_filtering total_read_pairs_before_filtering total_reads_after_filtering total_read_pairs_after_filtering total_bases_before_filtering total_bases_after_filtering read1_mean_length_before_filtering read1_mean_length_after_filtering read2_mean_length_before_filtering read2_mean_length_after_filtering q20_bases_before_filtering q20_bases_after_filtering q20_rate_before_filtering q20_rate_after_filtering q30_bases_before_filtering q30_bases_after_filtering q30_rate_before_filtering q30_rate_after_filtering gc_content_before_filtering gc_content_after_filtering adapter_trimmed_reads adapter_trimmed_bases -2489208 1244604.0 2489208 1244604.0 538461532 538461532 212 212 220 220 486388202 486388202 0.903292 0.903292 439107721 439107721 0.815486 0.815486 0.512001 0.512001 0 0 +2489208 1244604 2489208 1244604 538461532 538461532 212 212 220 220 486388202 486388202 0.903292 0.903292 439107721 439107721 0.815486 0.815486 0.512001 0.512001 0 0