Fastq filter and variant options

nanoporetech / pipeline-umi-amplicon

Workflow to prepare high accuracy single molecule consensus sequences from amplicon data using unique molecular identifiers

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Fastq filter and variant options #9

Closed SemiQuant closed 2 years ago

SemiQuant commented 3 years ago

I added a fastq filter options (min read length and average quality) using filtlong The user can also now pass options to the variant calling using the config file It runs as before when in defaults mode

I'd like to add two more options

Number of reads collapsed in the header of the bam file
Check that balance reads is working as its meant to

cjw85 commented 2 years ago

@SemiQuant,

Thanks for all these changes. I see you've been steadily adding to this. Is it ripe for merging? It seems to be in conflict with our default branch, I haven't checked why yet.

SemiQuant commented 2 years ago

hey @cjw85, I'm not 100% sure but I think if on default it still runs as before. Most of the conflicts seems to be in the environ file where I explicitly listed every package version as conda was failing to install correctly on some systems.