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Uncomment output paths in snM3C wdl #1113

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Uncomment output paths in snM3C wdl #1113

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17 changes: 9 additions & 8 deletions beta-pipelines/skylab/m3c/CondensedSnm3C.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -101,9 +101,6 @@ workflow WDLized_snm3C {

output {
#File MappingSummary = summary.MappingSummary
#File allcFiles = unique_reads_allc.
#File allc_CGNFiles = unique_reads_cgn_extraction.
#File UniqueAlign_cell_parser_picard_dedup = dedup_unique_bam_and_index_unique_bam.dedup_stats
#File SplitReads_cell_parser_hisat_summary = "?"
#File hicFiles = call_chromatin_contacts.chromatin_contact_stats
File trimmed_stats = Sort_and_trim_r1_and_r2.trim_stats_tar
Expand All @@ -120,9 +117,15 @@ workflow WDLized_snm3C {
File pos_sorted_bams = merge_original_and_split_bam_and_sort_all_reads_by_name_and_position.position_sorted_bam
File remove_overlap_read_parts_bam_tar = remove_overlap_read_parts.output_bam_tar
File dedup_unique_bam_and_index_unique_bam_tar = dedup_unique_bam_and_index_unique_bam.output_tar
File unique_reads_cgn_extraction_allc = unique_reads_cgn_extraction.output_allc_tar
File unique_reads_cgn_extraction_tbi = unique_reads_cgn_extraction.output_tbi_tar


# unique_reads_allc outputs
File allcFiles = unique_reads_allc.allc
File tbiFiles = unique_reads_allc.tbi
File allc_uniq_reads_stats = unique_reads_allc.allc_uniq_reads_stats

# unique_reads_cgn_extraction outputs
File allc_CGNFiles = unique_reads_cgn_extraction.output_allc_tar
File tbi_CGNFiles = unique_reads_cgn_extraction.output_tbi_tar
}
}

Expand Down Expand Up @@ -794,7 +797,6 @@ task unique_reads_allc {
}
}


task unique_reads_cgn_extraction {
input {
File allc_tar
Expand Down Expand Up @@ -859,7 +861,6 @@ task unique_reads_cgn_extraction {
}
}


#task summary {
# input {
# File trimmed_stats
Expand Down
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