Optional alignment subworkflow #83
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This was referenced Sep 18, 2023
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muffato
reviewed
Sep 18, 2023
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- You're missing
align = trueinconf/test_raw.config - I think it's confusing that the
inputchannel insubworkflows/local/coverage_stats.nfhas different shapes depending on a parameter. I would suggest that you move theSAMTOOLS_VIEWthat creates the CSI index toworkflows/blobtoolkit.nf(in theelseofif (params.align)) so thatch_alignedis always the BAM + CSI - There might be a problem with
bin/samplesheet.py: by allowing*.bamthere might be a clash duringSAMTOOLS_VIEWbecause the input and output files could be named the same ? Maybe theelseI was referring to in my previous point could check the file extension. If a BAM, then samtools index. If a CRAM, then samtools view ? - You need to add
pacbio_clras an allowed datatype inbin/samplesheet.py
These tests ran on the farm without errors using |
alxndrdiaz
approved these changes
Sep 28, 2023
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In the Snakemake version of the minimap2 alignment the input are reads in FASTQ format while in this case CRAM/BAM files are transformed to FASTA and aligned again using minimap2: What is the advantage for an user in doing so instead of simply using the input alignment file? Only wanted to clarify why this is useful.
The following test worked as expected with Nextflow 22.10.1:
nextflow run . -profile test_raw,singularity -ansi-log false
muffato
approved these changes
Sep 30, 2023
Prepare genome subworkflow
Unaligned files can also be in CRAM, BAM format. So if the user provides that and the align flag, now we can align it here and run the rest of the steps. Earlier, the user was required to provide aligned files. This is a step in making this pipeline independent. I can look at adding support for FASTQ as well, but after we sort out the config file. |
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Closes #79
This PR adds an optional alignment subworkflow. It replicates the one currently in BTK. It is not meant to be high quality alignments. Quick sub-optimal alignments are good enough for BTK and hence this approach with minimap is implemented. Please add suggestions for arguments to improve alignment with Minimap without introducing more extensive aligners like BWAmem.
I would especially like your input on
bin/samplesheet.py,subworkflows/local/coverage_stats.nf,subworkflows/local/minimap_alignment.nfandworkflows/blobtoolkit.nf