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added loops to summary
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@erinyoung
erinyoung committed May 9, 2024
1 parent 9536dff commit e954823
Showing 1 changed file with 37 additions and 94 deletions.
131 changes: 37 additions & 94 deletions donut_falls.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -1233,7 +1233,7 @@ process summary {
label "process_single"
publishDir "${params.outdir}/summary", mode: 'copy', saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
container 'staphb/multiqc:1.19'
time '10m'
time '30m'

input:
file(input)
Expand Down Expand Up @@ -1338,90 +1338,33 @@ process summary {
sorted_keys = sorted(dict.keys())
for key in sorted_keys:
final_dict[key] = {}
final_dict[key]['name'] = dict[key]['name']
final_dict[key]['number_of_reads'] = dict[key]['number_of_reads']
final_dict[key]['mean_read_length'] = dict[key]['mean_read_length']
final_dict[key]['mean_qual'] = dict[key]['mean_qual']
final_dict[key]['total_illumina_reads'] = dict[key]['total_illumina_reads']
final_dict[key]['nanopore_illumina_mash_distance'] = dict[key]['nanopore_illumina_mash_distance']
final_dict[key]['assemblers'] = dict[key]['assemblers']
for result_key in ['name', 'number_of_reads', 'mean_read_length', 'mean_qual', 'total_illumina_reads', 'nanopore_illumina_mash_distance', 'assemblers']:
final_dict[key][result_key] = dict[key][result_key]
if 'flye' in dict[key]['assemblers'].replace('dragonflye','dragon'):
if 'flye' in dict[key].keys():
final_dict[key]['flye_total_length'] = dict[key]['flye']['total_length']
final_dict[key]['flye_num_contigs'] = dict[key]['flye']['num_contigs']
final_dict[key]['flye_circ_contigs'] = dict[key]['flye']['circ_contigs']
final_dict[key]['flye_coverage'] = dict[key]['flye']['coverage']
final_dict[key]['flye_unmapped_nanopore'] = dict[key]['flye']['unmapped_nanopore']
final_dict[key]['flye_unmapped_nanopore_pc'] = dict[key]['flye']['unmapped_nanopore_pc']
final_dict[key]['flye_unmapped_illumina'] = dict[key]['flye']['unmapped_illumina']
final_dict[key]['flye_unmapped_illumina_pc'] = dict[key]['flye']['unmapped_illumina_pc']
final_dict[key]['flye_busco'] = dict[key]['flye']['busco']
final_dict[key]['flye_busco_polished'] = dict[key]['flye']['busco_pypolca']
final_dict[key]['flye_quality_before_polishing'] = dict[key]['flye']['Consensus_Quality_Before_Polishing']
final_dict[key]['flye_QV_before_polishing'] = dict[key]['flye']['Consensus_QV_Before_Polishing']
else:
final_dict[key]['flye_total_length'] = 0
final_dict[key]['flye_num_contigs'] = 0
final_dict[key]['flye_circ_contigs'] = 0
final_dict[key]['flye_coverage'] = 0
final_dict[key]['flye_unmapped_nanopore'] = 0
final_dict[key]['flye_unmapped_nanopore_pc'] = 0
final_dict[key]['flye_unmapped_illumina'] = 0
final_dict[key]['flye_unmapped_illumina_pc'] = 0
final_dict[key]['flye_busco'] = 'NF'
final_dict[key]['flye_busco_polished'] = 'NF'
final_dict[key]['flye_quality_before_polishing'] = 0
final_dict[key]['flye_QV_before_polishing'] = 0
if 'raven' in dict[key]['assemblers']:
if 'raven' in dict[key].keys():
final_dict[key]['raven_total_length'] = dict[key]['raven']['total_length']
final_dict[key]['raven_num_contigs'] = dict[key]['raven']['num_contigs']
final_dict[key]['raven_circ_contigs'] = dict[key]['raven']['circ_contigs']
final_dict[key]['raven_coverage'] = dict[key]['raven']['coverage']
final_dict[key]['raven_unmapped_nanopore'] = dict[key]['raven']['unmapped_nanopore']
final_dict[key]['raven_unmapped_nanopore_pc'] = dict[key]['raven']['unmapped_nanopore_pc']
final_dict[key]['raven_unmapped_illumina'] = dict[key]['raven']['unmapped_illumina']
final_dict[key]['raven_unmapped_illumina_pc'] = dict[key]['raven']['unmapped_illumina_pc']
final_dict[key]['raven_busco'] = dict[key]['raven']['busco']
final_dict[key]['raven_busco_polished'] = dict[key]['raven']['busco_pypolca']
final_dict[key]['raven_quality_before_polishing'] = dict[key]['raven']['Consensus_Quality_Before_Polishing']
final_dict[key]['raven_QV_before_polishing'] = dict[key]['raven']['Consensus_QV_Before_Polishing']
else:
final_dict[key]['raven_total_length'] = 0
final_dict[key]['raven_num_contigs'] = 0
final_dict[key]['raven_circ_contigs'] = 0
final_dict[key]['raven_coverage'] = 0
final_dict[key]['raven_unmapped_nanopore'] = 0
final_dict[key]['raven_unmapped_nanopore_pc'] = 0
final_dict[key]['raven_unmapped_illumina'] = 0
final_dict[key]['raven_unmapped_illumina_pc'] = 0
final_dict[key]['raven_busco'] = 'NF'
final_dict[key]['raven_busco_polished'] = 'NF'
final_dict[key]['raven_quality_before_polishing'] = 0
final_dict[key]['raven_QV_before_polishing'] = 0
results = ['total_length', 'num_contigs', 'circ_contigs', 'coverage', 'unmapped_nanopore', 'unmapped_nanopore_pc', 'unmapped_illumina', 'unmapped_illumina_pc']
for assembler in ['flye', 'raven']:
if assembler in dict[key]['assemblers'].replace('dragonflye','dragon'):
if assembler in dict[key].keys():
for result in results + ['busco']:
final_dict[key][assembler + '_' + result] = dict[key][assembler][result]
final_dict[key][assembler + '_busco_polished'] = dict[key][assembler]['busco_pypolca']
final_dict[key][assembler + '_quality_before_polishing'] = dict[key][assembler]['Consensus_Quality_Before_Polishing']
final_dict[key][assembler + '_QV_before_polishing'] = dict[key][assembler]['Consensus_QV_Before_Polishing']
else:
for result in results + ['quality_before_polishing', 'QV_before_polishing' ]:
final_dict[key][assembler + '_' + result] = 0
for result in ['busco', 'busco_polished']:
final_dict[key][assembler + '_' + result] = 'NF'
if 'unicycler' in dict[key]['assemblers']:
if 'unicycler' in dict[key].keys():
final_dict[key]['unicycler_total_length'] = dict[key]['unicycler']['total_length']
final_dict[key]['unicycler_num_contigs'] = dict[key]['unicycler']['num_contigs']
final_dict[key]['unicycler_circ_contigs'] = dict[key]['unicycler']['circ_contigs']
final_dict[key]['unicycler_coverage'] = dict[key]['unicycler']['coverage']
final_dict[key]['unicycler_unmapped_nanopore'] = dict[key]['unicycler']['unmapped_nanopore']
final_dict[key]['unicycler_unmapped_nanopore_pc'] = dict[key]['unicycler']['unmapped_nanopore_pc']
final_dict[key]['unicycler_unmapped_illumina'] = dict[key]['unicycler']['unmapped_illumina']
final_dict[key]['unicycler_unmapped_illumina_pc'] = dict[key]['unicycler']['unmapped_illumina_pc']
final_dict[key]['unicycler_busco'] = dict[key]['unicycler']['busco']
for result in results + [ 'busco']:
final_dict[key]['unicycler_' + result] = dict[key]['unicycler'][result]
else:
final_dict[key]['unicycler_total_length'] = 0
final_dict[key]['unicycler_num_contigs'] = 0
final_dict[key]['unicycler_circ_contigs'] = 0
final_dict[key]['unicycler_coverage'] = 0
final_dict[key]['unicycler_unmapped_nanopore'] = 0
final_dict[key]['unicycler_unmapped_nanopore_pc'] = 0
final_dict[key]['unicycler_unmapped_illumina'] = 0
final_dict[key]['unicycler_unmapped_illumina_pc'] = 0
for result in results:
final_dict[key]['unicycler_' + result] = 0
final_dict[key]['unicycler_busco'] = 'NF'
w = csv.DictWriter(tsv, final_dict[key].keys(), delimiter='\\t')
Expand Down Expand Up @@ -1464,19 +1407,19 @@ process summary {
final_results[key]['name'] = key
# from nanostas
final_results[key]['number_of_reads'] = nanoplot_dict[key]['number_of_reads']
final_results[key]['mean_read_length'] = nanoplot_dict[key]['mean_read_length']
final_results[key]['mean_qual'] = nanoplot_dict[key]['mean_qual']
final_results[key]['number_of_reads'] = int(nanoplot_dict[key]['number_of_reads'])
final_results[key]['mean_read_length'] = float(nanoplot_dict[key]['mean_read_length'])
final_results[key]['mean_qual'] = float(nanoplot_dict[key]['mean_qual'])
# from fastp
if key in fastp_dict.keys():
final_results[key]['total_illumina_reads'] = fastp_dict[key]
final_results[key]['total_illumina_reads'] = int(fastp_dict[key])
else:
final_results[key]['total_illumina_reads'] = 0
# from mash
if key in mash_dict.keys():
final_results[key]['nanopore_illumina_mash_distance'] = mash_dict[key]['dist']
final_results[key]['nanopore_illumina_mash_distance'] = float(mash_dict[key]['dist'])
else:
final_results[key]['nanopore_illumina_mash_distance'] = 'NF'
Expand All @@ -1503,21 +1446,21 @@ process summary {
# circulocov results
if key + '_' + assembler in circulocov_dict.keys():
if 'coverage' in circulocov_dict[key + '_' + assembler].keys():
final_results[key][assembler]['coverage'] = circulocov_dict[key + '_' + assembler]['coverage']
final_results[key][assembler]['coverage'] = float(circulocov_dict[key + '_' + assembler]['coverage'])
else:
final_results[key][assembler]['coverage'] = 'NF'
if 'unmapped_nanopore' in circulocov_dict[key + '_' + assembler].keys():
final_results[key][assembler]['unmapped_nanopore'] = circulocov_dict[key + '_' + assembler]['unmapped_nanopore']
final_results[key][assembler]['unmapped_nanopore_pc'] = '{:.2f}'.format(int(final_results[key][assembler]['unmapped_nanopore']) / int(nanoplot_dict[key]['number_of_reads']) * 100)
final_results[key][assembler]['unmapped_nanopore'] = int(circulocov_dict[key + '_' + assembler]['unmapped_nanopore'])
final_results[key][assembler]['unmapped_nanopore_pc'] = float('{:.2f}'.format(int(final_results[key][assembler]['unmapped_nanopore']) / int(nanoplot_dict[key]['number_of_reads']) * 100))
else:
final_results[key][assembler]['unmapped_nanopore'] = 'NF'
final_results[key][assembler]['unmapped_nanopore_pc'] = 'NF'
if 'unmapped_illumina' in circulocov_dict[key + '_' + assembler].keys():
final_results[key][assembler]['unmapped_illumina'] = circulocov_dict[key + '_' + assembler]['unmapped_illumina']
final_results[key][assembler]['unmapped_illumina'] = int(circulocov_dict[key + '_' + assembler]['unmapped_illumina'])
if 'total_illumina_reads' in final_results[key].keys() and final_results[key]['total_illumina_reads'] > 0:
final_results[key][assembler]['unmapped_illumina_pc'] = '{:.2f}'.format(int(final_results[key][assembler]['unmapped_illumina']) / int(final_results[key]['total_illumina_reads']) * 100 )
final_results[key][assembler]['unmapped_illumina_pc'] = float('{:.2f}'.format(int(final_results[key][assembler]['unmapped_illumina']) / int(final_results[key]['total_illumina_reads']) * 100 ))
else:
final_results[key][assembler]['unmapped_illumina_pc'] = 0.0
else:
Expand All @@ -1542,17 +1485,17 @@ process summary {
# pypolca results
if key + '_' + assembler in pypolca_dict.keys():
if 'Consensus_Quality_Before_Polishing' in pypolca_dict[key + '_' + assembler].keys():
final_results[key][assembler]['Consensus_Quality_Before_Polishing'] = pypolca_dict[key + '_' + assembler]['Consensus_Quality_Before_Polishing']
final_results[key][assembler]['Consensus_Quality_Before_Polishing'] = float(pypolca_dict[key + '_' + assembler]['Consensus_Quality_Before_Polishing'])
else:
final_results[key][assembler]['Consensus_Quality_Before_Polishing'] = 'NF'
if 'Consensus_QV_Before_Polishing' in pypolca_dict[key + '_' + assembler].keys():
final_results[key][assembler]['Consensus_QV_Before_Polishing'] = pypolca_dict[key + '_' + assembler]['Consensus_QV_Before_Polishing']
final_results[key][assembler]['Consensus_QV_Before_Polishing'] = float(pypolca_dict[key + '_' + assembler]['Consensus_QV_Before_Polishing'])
else:
final_results[key][assembler]['Consensus_QV_Before_Polishing'] = 'NF'
elif assembler != 'unicycler':
final_results[key][assembler]['Consensus_Quality_Before_Polishing'] = 0
final_results[key][assembler]['Consensus_QV_Before_Polishing'] = 0
final_results[key][assembler]['Consensus_Quality_Before_Polishing'] = 0.0
final_results[key][assembler]['Consensus_QV_Before_Polishing'] = 0.0
final_file(final_results)
tsv_file(final_results)
Expand Down

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