Np add single end r1 r2 mapping dna mode and merge sort split reads by name #1092
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…and_merge_sort_split_reads_by_name
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…dna_mode_and_merge_sort_split_reads_by_name' into np_add_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name
ekiernan
approved these changes
Oct 11, 2023
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| for file in "${R1_files[@]}"; do | ||
| sample_id=$(basename "$file" ".hisat3n_dna.split_reads.R1.fastq") | ||
| hisat-3n /cromwell_root/reference/hg38 -q -U ${sample_id}.hisat3n_dna.split_reads.R1.fastq --directional-mapping-reverse --base-change C,T --no-repeat-index --no-spliced-alignment --no-temp-splicesite -t --new-summary --summary-file ${sample_id}.hisat3n_dna_split_reads_summary.R1.txt --threads 11 | samtools view -b -q 10 -o "${sample_id}.hisat3n_dna.split_reads.R1.bam" |
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Should we split this line up like we do for the parameters for other tools, so that each parameter is on it's own line?
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that would probably make it more readable (and consistent with the rest of warp)
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yup totally missed this. will reformat!
…and_merge_sort_split_reads_by_name
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jessicaway
reviewed
Oct 11, 2023
| @@ -452,8 +454,11 @@ task Split_unmapped_reads { | |||
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| # wait 15 seconds for the files to be written | |||
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was this causing issues? weird
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yes, the tar command on line 461 kept complaining about the files being changed as it was tarring things up... Im not sure why the tar command would even start up if the previous python command block wasn't finished writing out the files? but the sleep 15 seemed to help
jessicaway
approved these changes
Oct 11, 2023
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| for file in "${R1_files[@]}"; do | ||
| sample_id=$(basename "$file" ".hisat3n_dna.split_reads.R1.fastq") | ||
| hisat-3n /cromwell_root/reference/hg38 -q -U ${sample_id}.hisat3n_dna.split_reads.R1.fastq --directional-mapping-reverse --base-change C,T --no-repeat-index --no-spliced-alignment --no-temp-splicesite -t --new-summary --summary-file ${sample_id}.hisat3n_dna_split_reads_summary.R1.txt --threads 11 | samtools view -b -q 10 -o "${sample_id}.hisat3n_dna.split_reads.R1.bam" |
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that would probably make it more readable (and consistent with the rest of warp)
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| for file in "${R2_files[@]}"; do | ||
| sample_id=$(basename "$file" ".hisat3n_dna.split_reads.R2.fastq") | ||
| hisat-3n /cromwell_root/reference/hg38 -q -U ${sample_id}.hisat3n_dna.split_reads.R2.fastq --directional-mapping --base-change C,T --no-repeat-index --no-spliced-alignment --no-temp-splicesite -t --new-summary --summary-file ${sample_id}.hisat3n_dna_split_reads_summary.R2.txt --threads 11 | samtools view -b -q 10 -o "${sample_id}.hisat3n_dna.split_reads.R2.bam" |
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Same here (split the command over multiple lines for readability and consistency)
…dna_mode_and_merge_sort_split_reads_by_name' into np_add_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name
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…and_merge_sort_split_reads_by_name
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nikellepetrillo
deleted the
np_add_single_end_r1_r2_mapping_dna_mode_and_merge_sort_split_reads_by_name
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khajoue2
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Nov 2, 2023
* Update Loom_schema.md (#1080) * Lk dynamically select barcode orientation (#1086) * Added dynamic barcode selection to the ATAC FastqProcess task * Np pd 2327 separate unmapped reads (#1084) * add separate unmapped reads task * clean up * add splut unmapped reads (#1087) * KM Update metrics descriptions (#1088) * Update metrics descriptions * Update Loom_schema.md * Update Loom_schema.md * Add TagSort and definitions * Km fix broken links in docs (#1090) * Update Terra link address * Fix links to snaptools Docker * Fixed link to SS2 overview * Update link to snM3C test_inputs directory * Fixed link to Multiome test data * Fix link to loom_to_h5ad.py script * Fix link to loom creation script * Fixed links * Lk pd 2363 join barcodes (#1089) Added GEX and ATAC whitelist barcodes to both ATAC and GEX h5ad files so that barcodes that can be joined. * Update UnmappedBamToAlignedBam.wdl (#1070) Changed MarkDuplicates task to use Float size(Array[File], [String]) * Np add single end r1 r2 mapping dna mode and merge sort split reads by name (#1092) * echo whitelistnew task * rearranging * cleaning up * cleaning up * cleaning up * formatting --------- Co-authored-by: aawdeh <[email protected]> * Lk pd 2374 update whitelist (#1093) Updated path of multiome whitelists * Km fix broken links in WARP docs (#1097) * Update Multiome README * Update broken links in docs * Update get-started.md * Update broken bookmarks in docs * Remove the dropna and MATCH columns from JoinBarcodes (#1098) * Remove the dropna and MATCH columns from JoinBarcodes * PD-2379-add_remove_overlap_read_parts_task (#1094) * Added merge_original_and_split_bam_sort_all_reads_name_and_position * Cleaning up a few ls and pwds, adding echos * add task dedup_unique_bam_and_index_unique_bam (#1103) * Km atac h5ad overview (#1102) * Create count-matrix-overview.md * Update count-matrix-overview.md * Add barcode column names Add the column names containing the GEX and ATAC barcodes in the output h5ad files to the Multiome README * Update count-matrix-overview.md * Update README.md * Km doc updates (#1100) * Update links in Optimus Overview doc * Update version numbers in READMEs * Update count-matrix-overview.md * Update count-matrix-overview.md * Add link to SnapATAC2 import_data function * Update count-matrix-overview.md * Update website/docs/Pipelines/ATAC/count-matrix-overview.md Co-authored-by: ekiernan <[email protected]> * Update website/docs/Pipelines/ATAC/count-matrix-overview.md Co-authored-by: ekiernan <[email protected]> * Update website/docs/Pipelines/ATAC/count-matrix-overview.md Co-authored-by: ekiernan <[email protected]> --------- Co-authored-by: ekiernan <[email protected]> * Add unique_reads_allc * Update CondensedSnm3C.wdl * Km add atac rrid and update multiome readme (#1109) * Update Multiome README * Update pipeline version output * Update README.md * Update inputs to CramToUnmappedBam test (#1104) * update paths to input files * Add unique_reads_cgn_extraction task (#1107) --------- Co-authored-by: ekiernan <[email protected]> Co-authored-by: Nikelle Petrillo <[email protected]> Co-authored-by: Kaylee Mathews <[email protected]> Co-authored-by: aawdeh <[email protected]> Co-authored-by: ekiernan <[email protected]> Co-authored-by: Jessica Way <[email protected]>
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