tgen / tempe

A container focused and streamlined iteration of the Phoenix pipeline
GNU General Public License v3.0
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Stats output name not consistent - #1 #27

Closed PedalheadPHX closed 1 year ago

PedalheadPHX commented 1 year ago

https://github.com/tgen/tempe/blob/ffa81371cdb3246f66c8621abc39609a618c615f/modules/dna_alignment/fgbio_umi.jst#L68 and https://github.com/tgen/tempe/blob/ffa81371cdb3246f66c8621abc39609a618c615f/modules/dna_alignment/fgbio_umi.jst#L191

Need to update stats filenames to be consistent

-rw-r--r-- 1 devjetstream domainuser 0 Apr 22 11:45 NC_0037_1_PB_KMS27_T8_TEF2P.bwa.bam.bamstats.txt -rw-r--r-- 1 devjetstream domainuser 111K Apr 22 11:45 NC_0037_1_PB_KMS27_T8_TEF2P.bwa.bam.idxstats.txt -rw-r--r-- 1 devjetstream domainuser 214K Apr 22 11:46 NC_0037_1_PB_KMS27_T8_TEF2P.bwa.bam.snpSniffer.vcf -rw-r--r-- 1 devjetstream domainuser 101K Apr 22 11:46 NC_0037_1_PB_KMS27_T8_TEF2P_K33252.bwa.bam.idxstats.json -rw-r--r-- 1 devjetstream domainuser 111K Apr 22 11:45 NC_0037_1_PB_KMS27_T8_TEF2P_K33252.bwa.bam.idxstats.txt -rw-r--r-- 1 devjetstream domainuser 214K Apr 22 11:46 NC_0037_1_PB_KMS27_T8_TEF2P_K33252.bwa.bam.snpSniffer.vcf -rw-r--r-- 1 devjetstream domainuser 290 Apr 22 10:50 NC_0037_1_PB_KMS27_T8_UMIcorr_bwa_gd_hist.txt -rw-r--r-- 1 devjetstream domainuser 1.7K Apr 22 09:39 NC_0037_1_PB_KMS27_T8_UMIcorr_bwa.txt

likely needs to be something more like {{ sample.rgsm }}{{ sample.rglb }}{{ aligner }}.bam.umiCorr.txt {{ sample.rgsm }}{{ sample.rglb }}{{ aligner }}.bam.umiFamilySize.txt