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Tcoffee tcs #5288
Tcoffee tcs #5288
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getting the updates on tcoffee/align
…t lib and modified test for compressed
Description: This module uses t_coffee to compute the Transient Consistency Score (TCS). A metric used to assest the quality and conservation of the given MSA. It expects a msa as input and optionally a msa library. It outputs the TCS file in the score_ascii format of t_coffee and a simple csv reporting the overall TCS value for the given msa. |
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Looking good, just some minor remarks
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input: | ||
tuple val(meta), path(msa) | ||
tuple val(meta2), path(lib) |
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Why 2 input channels? It seems meta2 is not even used in the script
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You can optionally pass a lib file. And if you doyou pass it through a channel that created such library in an alignment step before, so it will have it is own meta anyway. It is not used because not needed. But it will be passed in case with the lib file.
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Okay, should be fine as is
def lib_arg = lib ? "-lib ${lib}" : "" | ||
def header = meta.keySet().join(",") | ||
def values = meta.values().join(",") | ||
def unzipped_name = msa.toString() - '.gz' |
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Align equal signs
Hm weird, locally prettier runs without any issues. |
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I see everything's fixed, good to go.
* master: Tcoffee tcs (nf-core#5288) Add and update - picard/gatk4 - addorreplacereadgroups (nf-core#5302) New module svtypersso (nf-core#5311)
* right ater execution of nf-core modules create * added compression compatibility * allocated for otional lib file and created scores csv file based on tcs output * compiled the meta.yml * added the test for msa and msa compressed * removed lib only option * fixed issue with filename extension after ungzip, wrote test for input lib and modified test for compressed * added direct export of TEMP dir, hopefully fixes error ongithub singularity * fixing trailing whitespaces
* right ater execution of nf-core modules create * added compression compatibility * allocated for otional lib file and created scores csv file based on tcs output * compiled the meta.yml * added the test for msa and msa compressed * removed lib only option * fixed issue with filename extension after ungzip, wrote test for input lib and modified test for compressed * added direct export of TEMP dir, hopefully fixes error ongithub singularity * fixing trailing whitespaces
* right ater execution of nf-core modules create * added compression compatibility * allocated for otional lib file and created scores csv file based on tcs output * compiled the meta.yml * added the test for msa and msa compressed * removed lib only option * fixed issue with filename extension after ungzip, wrote test for input lib and modified test for compressed * added direct export of TEMP dir, hopefully fixes error ongithub singularity * fixing trailing whitespaces
PR checklist
Closes #XXX
versions.yml
file.label
nf-core modules test <MODULE> --profile docker
nf-core modules test <MODULE> --profile singularity
nf-core modules test <MODULE> --profile conda
nf-core subworkflows test <SUBWORKFLOW> --profile docker
nf-core subworkflows test <SUBWORKFLOW> --profile singularity
nf-core subworkflows test <SUBWORKFLOW> --profile conda