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Missing conversion from bam to cram when starting from "--step prepare_recalibration" · Issue #1894 · nf-core/sarek · GitHub
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Hi all,
I'm trying to run Sarek from --step prepare_recalibration with bam files as input. It doesn't proceed to the BAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAM step due to the fact that the GATK4_APPLYBQSR.out.cram channel is empty, since bam input is emitted in GATK4_APPLYBQSR.out.bam instead. Maybe I'm missing something, but I don't see a conversion of the input bam files to cram format before feeding it to GATK4_APPLYBQSR when starting from prepare_recalibration? This might be related to this issue: #1875
As expected, changing line 39 in modules/nf-core/gatk4/applybqsr/main.nf from --output ${prefix}.${input.getExtension()}
to --output ${prefix}.cram
and therefore enforcing cram output for bam input solves the issue, so this indeed seems to be a bug.
Description of the bug
Hi all,
I'm trying to run Sarek from
--step prepare_recalibrationwith bam files as input. It doesn't proceed to theBAM_APPLYBQSR:CRAM_MERGE_INDEX_SAMTOOLS:MERGE_CRAMstep due to the fact that theGATK4_APPLYBQSR.out.cramchannel is empty, since bam input is emitted inGATK4_APPLYBQSR.out.baminstead. Maybe I'm missing something, but I don't see a conversion of the input bam files to cram format before feeding it toGATK4_APPLYBQSRwhen starting from prepare_recalibration? This might be related to this issue: #1875As expected, changing line 39 in modules/nf-core/gatk4/applybqsr/main.nf from
--output ${prefix}.${input.getExtension()}to
--output ${prefix}.cramand therefore enforcing cram output for bam input solves the issue, so this indeed seems to be a bug.
https://github.com/nf-core/sarek/milestone/11
Command used and terminal output
Relevant files
No response
System information
No response
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