🧠 adjust t1k memory

Author: dmiller15

tools/t1k.cwl

@@ -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' } }

workflows/kfdrc_alignment_wf.cwl

@@ -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."}
@@ -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

workflows/kfdrc_sentieon_alignment_wf.cwl

@@ -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."}
@@ -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