New module: angsd/dosaf#12359
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….args when using doSAF 2
…us add within test generation of angsd_syk.errors and angsd_FIN.indF
| tuple val(meta), path(bams), path(bam_indices) | ||
| tuple val(meta2), path(reference_fasta), path(reference_fai) | ||
| tuple val(meta3), path(ancestral_fasta), path(ancestral_fai) // Optional. Provides ancestral state for unfolded SFS. | ||
| tuple val(meta4), path(error_file) // Optional. Required for SYK model (-GL 4) only. | ||
| tuple val(meta5), path(inbreeding_coefficients) // Optional. Required for -doSAF 2 (inbreeding-aware mode). | ||
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do you need all these different meta maps?
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The only particularly useful one is the meta map associated with bam files, as would include population ID and associated samples. This would be used by downstream processes that consume output from angsd/dosaf. I will remove the other meta maps, unless you think meta maps should be included for fasta files? Is there any guidance on when meta maps should be provided?
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https://nf-co.re/docs/specifications/components/modules/general#use-of-meta-maps
you can also use the same meta map several times. the usage is a bit dependent on usual upstream and downstream processes.
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I have removed unnecessary meta maps in commit 802a9b9
…unnecessary meta maps, update meta.yml and tests accordingly.
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
Co-authored-by: Matthias Hörtenhuber <mashehu@users.noreply.github.com>
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@mashehu thanks for the suggested code improvements (especially the method for condensing the main code block!), these are now incorporated 😄 |
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This PR adds a new module
angsd/dosaffor estimating per-population site allele frequency likelihoods from BAM files using ANGSD's doSAF function (https://www.popgen.dk/angsd/index.php/SFS_Estimation). Outputs SAF files (.saf.idx, .saf.pos.gz, .saf.gz) which can be used for downstream site frequency spectrum (SFS) estimation, Fst calculation, and estimating population diversity statistics e.g. nucleotide diversity and Tajima's D.Test data for this module has been added: nf-core/test-datasets#2131
PR checklist
Closes #12185
topic: versions- See version_topicslabelnf-core modules test <MODULE> --profile dockernf-core modules test <MODULE> --profile singularitynf-core modules test <MODULE> --profile conda