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🧠 adjust t1k memory #143

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Sep 23, 2024
Merged

🧠 adjust t1k memory #143

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2 changes: 1 addition & 1 deletion tools/t1k.cwl
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Original file line number Diff line number Diff line change
Expand Up @@ -59,7 +59,7 @@ inputs:
output_read_assignment: { type: 'boolean?', inputBinding: { position: 12 , prefix: "--outputReadAssignment" }, doc: "Set to output the allele assignment for each read to prefix_assign.tsv file" }

threads: { type: 'int?', doc: "Num processing threads to use", default: 8, inputBinding: { position: 12, prefix: "-t" } }
ram: { type: 'int?', doc: "Num GB memory to make available", default: 16 }
ram: { type: 'int?', doc: "Num GB memory to make available", default: 32 }
outputs:
aligned_fasta: { type: 'File[]', outputBinding: { glob: '*_aligned_*.fa' } }
allele_tsv: { type: File, outputBinding: { glob: '*_allele.tsv' } }
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2 changes: 2 additions & 0 deletions workflows/kfdrc_alignment_wf.cwl
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Expand Up @@ -392,6 +392,7 @@ inputs:
hla_dna_gene_coords: {type: 'File?', doc: "FASTA file containing the coordinates of the HLA genes for DNA.", "sbg:suggestedValue": {
class: File, path: 6669ac8127374715fc3ba3c2, name: hla_v3.43.0_gencode_v39_dna_coord.fa}}
t1k_abnormal_unmap_flag: {type: 'boolean?', doc: "Set if the flag in BAM for the unmapped read-pair is nonconcordant"}
t1k_ram: {type: 'int?', doc: "GB of RAM to allocate to T1k." }
outputs:
cram: {type: File, outputSource: samtools_bam_to_cram/output, doc: "(Re)Aligned Reads File"}
gvcf: {type: 'File[]?', outputSource: generate_gvcf/gvcf, doc: "Genomic VCF generated from the realigned alignment file."}
Expand Down Expand Up @@ -655,6 +656,7 @@ steps:
valueFrom: $(self).t1k_hla
skip_post_analysis:
valueFrom: $(1 == 1)
ram: t1k_ram
out: [genotype_tsv]
samtools_bam_to_cram:
run: ../tools/samtools_bam_to_cram.cwl
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2 changes: 2 additions & 0 deletions workflows/kfdrc_sentieon_alignment_wf.cwl
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Expand Up @@ -182,6 +182,7 @@ inputs:
hla_dna_gene_coords: {type: 'File?', doc: "FASTA file containing the coordinates of the HLA genes for DNA.", "sbg:suggestedValue": {
class: File, path: 6669ac8127374715fc3ba3c2, name: hla_v3.43.0_gencode_v39_dna_coord.fa}}
t1k_abnormal_unmap_flag: {type: 'boolean?', doc: "Set if the flag in BAM for the unmapped read-pair is nonconcordant"}
t1k_ram: {type: 'int?', doc: "GB of RAM to allocate to T1k." }
outputs:
cram: {type: File, outputSource: sentieon_readwriter_bam_to_cram/output_reads, doc: "(Re)Aligned Reads File"}
gvcf: {type: 'File?', outputSource: generate_gvcf/gvcf, doc: "Genomic VCF generated from the realigned alignment file."}
Expand Down Expand Up @@ -368,6 +369,7 @@ steps:
skip_post_analysis:
valueFrom: $(1 == 1)
abnormal_unmap_flag: t1k_abnormal_unmap_flag
ram: t1k_ram
out: [genotype_tsv]
sentieon_readwriter_bam_to_cram:
run: ../tools/sentieon_ReadWriter.cwl
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