Remove gtex #299
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Remove gtex #299
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cgpu
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Dec 17, 2021
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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This PR:
Gen3-DRSdownload option toGTEXas not it is the only way to download GTEX files.