Dev v2.1 #287 - Simplify the Gen3-DRS download option #304
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@angarb to test with |
Vlad-Dembrovskyi
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Feb 3, 2022
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Pipeline is failing
https://cloudos.lifebit.ai/public/jobs/61fbfd418c574a01e8e960b4
Vlad-Dembrovskyi
suggested changes
Feb 3, 2022
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Another issue, at filter_manifest step:
https://cloudos.lifebit.ai/public/jobs/61fc0a9b8c574a01e8e9d0fa
Nextflow when running on GCP CloudOS probably cannot normally access the bin folder scripts. Either the container must have different options to run, and be set to the user as GCP nextflow user is with docker.runOptions or smth (tricky). Or the script has to be put inside container on path. Latter is easier.
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Vlad-Dembrovskyi
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Feb 22, 2022
ilevantis
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May 19, 2022
* Fixes env gtex issue #290 (#294) * Change env() to stdout to save sample_name in gen3_drs * Fix No such property: baseName for class: String * Gen3-DRS prints md5 "file is good" to log not stdout * Improves gen3-drs md5 error message * Changes gtex input to support new manifest file format [#289] (#296) * Updates ch_gtex_gen3_ids items #289 * Remove duplicate val(obj_id) in input of gen3-drs Co-authored-by: cgpu <38183826+cgpu@users.noreply.github.com> * Comments our fasta requirement for gen3-drs input (#297) * Comments our fasta requirement for gen3-drs input * Update usage.md that genome_fasta is only for CRAM * Update usage.md typo * Fix missing file from path issue * change GLS executor from parameter to scope (#305) * Remove gtex (#299) * Remove mentions of old GTEX download option from main.nf * Remove mentions of old GTEX download option from help * Remove mentions of old GTEX download option from usage.md * Renames Gen3-DRS into new GTEX download option * Renames Gen3-DRS into new GTEX download opt in usage.md * Dev v2.1 #287 - Simplify the Gen3-DRS download option (#304) * Update usage.md * Update run_on_sumner.md * add dockerfile for csvtoolkit * add process to convert manifest json to csv * add process to filter manifest by file passed through --reads * update help message * fix bug on variable declaration * Update nextflow.config - fix typo * Revert "Merge branch 'master' into dev-v2.1-#287" This reverts commit be2c2ab, reversing changes made to 04285ef. * Update main.nf * patch projectDir error * Fix oublishDir path for manifest * Fix oublishDir path for manifest * Fix typo * Update filter_manifest.py * Update filter_manifest.py * fix bug on saving filenames that were not in manifest file * Update filter_manifest.py * remove logging of samples not found in manifest * Update filter_manifest.py * Makes filter_manifest txt output optional Co-authored-by: angarb <62404570+angarb@users.noreply.github.com> Co-authored-by: Vlad-Dembrovskyi <64809705+Vlad-Dembrovskyi@users.noreply.github.com> Co-authored-by: Vlad-Dembrovskyi <vlad@lifebit.ai> * Rename examples/gen3/README.md to examples/GTEX/README.md Editing folder name to match new "download_from" name. * Update and rename GEN3_DRS_config.md to GTEX_config.md Updating parameters * Delete examples/gen3 directory * Update usage.md Moving this information * Update README.md * Update README.md * Delete PRJNA453538.SraRunTable.txt Not needed * Delete MCF10_MYCER.datafiles.csv Not needed * Create reads.csv Adding reads.csv example * Update README.md * Create manifest.json Adding example manifest.json * Update README.md * Update run_on_cloudos.md * Update Copying_Files_From_Sumner_to_Cloud.md Made neater * Create Star_Index_Generation.md Co-authored-by: cgpu <38183826+cgpu@users.noreply.github.com> Co-authored-by: imendes93 <73831087+imendes93@users.noreply.github.com> Co-authored-by: angarb <62404570+angarb@users.noreply.github.com>
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Closes #287
Description
This PR adds the following alterations:
--manifestparameter with the input being the .json manifest file downloaded from GTEX--readsparameter receives a CSV file with samples for which the analysis will be limited to