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* add submitted_md5 column to SSF output * remove old unused code * Use BAM from submitted_ftp when no fastq_ftp is provided. * Add gsa to ssf script (#78) * first version of gsa_to_ssf script * added some type hints, removed old add_column function * made proposed changes to script. Added ssf data * mf * started janno * added dating information * [automated] Create package recipe from SSF files * mf * Revert "[automated] Create package recipe from SSF files" This reverts commit 726e114. * Revert "added dating information" This reverts commit d5e6596. * Revert "started janno" This reverts commit 94cd549. * remove 2025_Liu_ShanDong.ssf * add submitted_md5 column * WIP. refactor script. add TODOs * add main. restructure code a bit. new excel to ssf funct * update script. * validate submitted_ftp and md5. Allow missing fastq_ftp. bump version * indentation error --------- Co-authored-by: kavlahkaff <de28oser@studserv.uni-leipzig.de> Co-authored-by: delphis-bot <delphis-bot@poseidon-adna.org> * Bump config versions to 0.5.0 * Bump versions --------- Co-authored-by: kavlahkaff <de28oser@studserv.uni-leipzig.de> Co-authored-by: delphis-bot <delphis-bot@poseidon-adna.org>
TCLamnidis
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May 20, 2025
* add submitted_md5 column to SSF output * remove old unused code * Use BAM from submitted_ftp when no fastq_ftp is provided. * Add gsa to ssf script (#78) * first version of gsa_to_ssf script * added some type hints, removed old add_column function * made proposed changes to script. Added ssf data * mf * started janno * added dating information * [automated] Create package recipe from SSF files * mf * Revert "[automated] Create package recipe from SSF files" This reverts commit 726e114. * Revert "added dating information" This reverts commit d5e6596. * Revert "started janno" This reverts commit 94cd549. * remove 2025_Liu_ShanDong.ssf * add submitted_md5 column * WIP. refactor script. add TODOs * add main. restructure code a bit. new excel to ssf funct * update script. * validate submitted_ftp and md5. Allow missing fastq_ftp. bump version * indentation error --------- Co-authored-by: kavlahkaff <de28oser@studserv.uni-leipzig.de> Co-authored-by: delphis-bot <delphis-bot@poseidon-adna.org> * Bump config versions to 0.5.0 * Bump versions * fix SSF to TSV conversion when only BAMs are available. --------- Co-authored-by: kavlahkaff <de28oser@studserv.uni-leipzig.de> Co-authored-by: delphis-bot <delphis-bot@poseidon-adna.org>
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Linked to #68 #69
This PR adds a script to pull SSF info from the GSA.