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…man-lab/Long-Read-Proteogenomics into adds-nextflow-boilerplate
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cgpu
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cgpu
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cgpu
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Nov 24, 2020
To respect the rule, "we do not choose to modify cod ebehaviour by commenting in and out code chunks",
cgpu
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gsheynkman
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gsheynkman
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* Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Adds Author Name in README (#15) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * add long read info basics * gui app manifest gitignore fix * Adds @trishorts name in README.md (#18) * add author name to readme.md * add one line to refresh commit * add author name Co-authored-by: Michael Shortreed <[email protected]> Co-authored-by: cgpu <[email protected]> * Adds @gsheynkman name to README.md (#16) * Added authorname in README Co-authored-by: cgpu <[email protected]> * Adds Rachel Miller to the author names in the README (#14) * Adds Rachel Miller to the author names in the README * Minor typo Co-authored-by: cgpu <[email protected]> * added author and ORCID (#12) Co-authored-by: cgpu <[email protected]> * Refined database orig code (#29) * Add initial code to extract and cluster pacbio protein sequences, based on input from LR_ORFCalling * aggregation of FL and CPM by cluster Co-authored-by: Robert Millikin <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> * Bj8th orf calling (#25) * Add author name in README.md * orf calling updted to run from command line Co-authored-by: gsheynkman <[email protected]> * Adds nextflow files and folders based on nf-core template (#26) * Adds nf-core template for nextflow pips * Cleans up template main.nf and adds swag cli message * Updates nextflow.config * Adds Dockerfile and env yaml updates * Removes redundant files from assets * Deleted nf schema json * Removes redundant configs * Updates README with template structure * Updates docs/ * Updates repo name in changelog * Updates template test.config * Adds bin folder and template wrapper R script * Adds pbccs in env.yml * Changes the location of pipeline info, logs * Adds .github folder * Removes redundant files from GH actions * Removes AWS tests * Adds misspelling test * Removes linting.yml * Removes igenomes config * Adds tentative LICENSE (MIT) * Adds nudge for asking help via GH issues * added pull scripts from the zenodo site * weighted protein inference * fixes * remove script to hopefully avoid merge conflict.. * update mzLib * require equal long read weight for indistinguishable proteins * add contrib * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * update main readme with author names (#38) * update README contributions * new readme * fix minor errors in readme (#40) * update README contributions * new readme * fix readme errors * excel compatible tsv by default * accept thermo license by default * Updated READMEs, uploaded scripts for isoform mapping, protein clustering. (#41) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * delete files that shouldn't be part of the previous commit, old scripts accidentally put in DatabaseAnnotation * updated contributions (#44) * Attempt to create a container for blast mapping process within nextflow. (#48) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * adding cpat and transdecoder containers (#36) * added pull scripts from the zenodo site * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Added commands to run CPAT. 'output' directory to .gitignore. (#53) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Add nextflow-related files, sundries. (#55) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Adding Simi's transcriptomic and peptide analysis scripts. (#56) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Gloria adding Simi's transcriptome analysis and peptide analysis scripts. * argparse modification (#57) * adds lr_orfcalling.nf and lr_orfcalling_nextflow.config in the module LR_ORFCalling (#59) * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * created local lr_orfcalling.nf and _nextflow.config to aid in local testing and debugging before final merge into pipeline * adding main.nf and nextflow.config * Protein Inference Analysis Module Custom Script (#64) * Adds Rachel Miller to the author names in the README * custom script for the comparison of protein group output from MetaMorpheus searches using different protein database reference models * Add files via upload Update of peptide analysis jupyter notebook script * Need to merge with latest dev (disregarding differences in dev_gloria, which are outdated) (#67) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Gloria adding Simi's transcriptome analysis and peptide analysis scripts. * Update orf_calling.py Removed a line to match spacing with the py file in dev. * Convert jupyter notebook into python * ORF Calling - bug fix (#70) * argparse modification * small import bug fix Co-authored-by: gsheynkman <[email protected]> * Update README.md (#65) * Update README.md * Update README.md spelling fixes * Update README.md * ORF Filtering bug fixes and RefineDB (#71) * argparse modification * small import bug fix * fixed bugs in orf_filter. module for refining db * refine orf working Co-authored-by: gsheynkman <[email protected]> * Adds Dockerfile, environment.yml for SQANTI3 (#72) * Adds Dockerfile, environment.yml for SQANTI3 * Improves container files Co-authored-by: EC2 Default User <[email protected]> * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * Updated peptide analysis file (#66) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Add files via upload Update of peptide analysis jupyter notebook script * Convert jupyter notebook into python * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * 6frm readme (#45) * Add initial code to extract and cluster pacbio protein sequences, based on input from LR_ORFCalling * Started code for protein group mapping * add toy tables for the protein inference mapping * edited 6frm translate readme * delete mock files for protein inference (protein group) comparisons. Rachel and Kyndalanne have continued to work on this and these may be outdated. Co-authored-by: Robert Millikin <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> * Protein Inference (#74) * Separate module for greedy protein inference * protein_inference bug fix * added rescue to greedy algorithm * connected peptides changed to set * small bug fix. cleaned up notebook * Removed unnecessary files from Transcriptome Module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module (#75) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Add files via upload Update of peptide analysis jupyter notebook script * Convert jupyter notebook into python * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * Removed unnecessary files from Transcriptome Module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Simi and Gloria - Update referencetable, transcriptome, and peptide modules (#78) * Files in progress to create three modules: ReferenceTables, TranscriptomeAnalysis, PeptideAnalysis. Also, debugged orf_calling.py, found that minus strand ORFs not included. * Prepared a script that makes reference tables * Updated Transcriptomic Script * Updated Transcriptomic Script (#77) Co-authored-by: kyuubi430 <[email protected]> * Remove files for making three modules with simi. * Cleaned up referencetable module, Simi to edit. * Modified Reference Tables Script * Deleted plots. * Simi and Gloria finalized the prepare_reference_tables. Works on commandline. Correct outputs to results/PG_ReferenceTables. * Small edits to peptide_analysis, not done, push to Simi. * Modified the names out output files from Prepare Reference Tabe script * Changed file names in reference tables script and modified the transcriptome summary * Delete unneeded files in transcriptome summary module. * Finalized ReferenceTables. tested Transcriptome Summary. Started modifying the PeptideAnalysis. * Made the transcriptome summary script command line executable * Made the peptide analysis script command line runnable * In process of modifying MMprocessing script * Move scripts between TranscriptomeSummary and PeptideAnalysis modules. Code related to MM peptide/protein processing will now be exclusively in PeptideAnalysis. * Added fasta/tsv and the results directory to gitignore * Delete jurkat_orf_refined.fasta Don't want to include *fasta in pull request. * Delete genes_in_refined.tsv Don't want to include *tsv output file in PR. Added *tsv to gitignore, so shouldn't upload in future PR. Co-authored-by: kyuubi430 <[email protected]> * Adds modules nextflow pseudocode (#79) * Adds nf-core template for nextflow pips * Cleans up template main.nf and adds swag cli message * Updates nextflow.config * Adds Dockerfile and env yaml updates * Removes redundant files from assets * Deleted nf schema json * Removes redundant configs * Updates README with template structure * Updates docs/ * Updates repo name in changelog * Updates template test.config * Adds bin folder and template wrapper R script * Adds pbccs in env.yml * Changes the location of pipeline info, logs * Adds .github folder * Removes redendant files from GH actions * Updates CONTRIBUTING.md * Updates ISSUE_TEMPLATE * Update PULL_REQUEST_TEMPLATE.md * Removes AWS tests * Adds misspelling test * Removes linting.yml * Corrects typo * Removes igenomes config * Fixes typos caught by review-dog * Adds tentative LICENSE * Adds environment.yml with pandas, numpy, biopython * Adds CCS process * Adds pbbam (required for ccs --chunk subsequent routine) * Adds pbindex, ccs processes (w/ parallel --chunks) * Removes redundant bai (pbi is needed) * Adds temp process mock ccs and flag for testing * Deletes commented out section To respect the rule, "we do not choose to modify cod ebehaviour by commenting in and out code chunks", * Makes the section note more informative * Dev rmmiller protein inference (#83) * Adds Rachel Miller to the author names in the README * custom script for the comparison of protein group output from MetaMorpheus searches using different protein database reference models * Make protein inference analysis script command line executable * spelling fixes * Update PI_proteinInferenceAnalysis.py fix merge conflicts * Adds nextflow referencetable, notes to SQANTI module. (#88) * Initiated files for nextflowifying reference-table module. * Add nextflow code for reference table module. Successfully run on Lifebit/CloudOS. * Rename transcript script. Add notes on requirements and commands to run SQANTI. * Adds nextflow refined db (#80) * Moves refine_orfs.py * Restores tsv vs csv in refine_orfs.py * Adds Nextflow files for refined db generation * Refactor Dockerfile to eliminate duplication of env name * Updates README.md in the modules/LR_ORFCalling subdirectory and lr_orfcalling.nf and lr_orfcalling_nextflow.config (#63) * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * created local lr_orfcalling.nf and _nextflow.config to aid in local testing and debugging before final merge into pipeline * adding main.nf and nextflow.config * added to README.md instructions for executing nextflow within a jupyter notebook for debugging * Update README.md * Update README.md * Updates ORF calling Nextflow files (#73) * Updates ORF calling Nextflow snippet * Deletes redundant global container definition * Removes superfluous new line * Clean up of comments * Updates channel syntax to simplify to 1 line * Adds TransDecoder in log.info summary * Adds nextflow_run.sh with commands, expected exits * Improves code readability, adds file exists check Co-authored-by: EC2 Default User <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: EC2 Default User <[email protected]> Co-authored-by: bj8th <[email protected]> * Add nextflow io (#100) * added input output to readmes and modified to run via main * refine database readme * pull request changes made * Clean up peptideanalysismodule (#99) * Clean up peptide analysis module. * Remove README * Bj8th readme (#102) * added readme information to several modules. updated modules to run from command line * added source modules Co-authored-by: kyuubi430 <[email protected]> Co-authored-by: kyuubi430 <[email protected]> Co-authored-by: rob <[email protected]> Co-authored-by: trishorts <[email protected]> Co-authored-by: Michael Shortreed <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: gsheynkman <[email protected]> Co-authored-by: rmmiller22 <[email protected]> Co-authored-by: Anne Deslattes Mays <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: EC2 Default User <[email protected]>
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* Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Adds Author Name in README (#15) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * add long read info basics * gui app manifest gitignore fix * Adds @trishorts name in README.md (#18) * add author name to readme.md * add one line to refresh commit * add author name Co-authored-by: Michael Shortreed <[email protected]> Co-authored-by: cgpu <[email protected]> * Adds @gsheynkman name to README.md (#16) * Added authorname in README Co-authored-by: cgpu <[email protected]> * Adds Rachel Miller to the author names in the README (#14) * Adds Rachel Miller to the author names in the README * Minor typo Co-authored-by: cgpu <[email protected]> * added author and ORCID (#12) Co-authored-by: cgpu <[email protected]> * Refined database orig code (#29) * Add initial code to extract and cluster pacbio protein sequences, based on input from LR_ORFCalling * aggregation of FL and CPM by cluster Co-authored-by: Robert Millikin <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> * Bj8th orf calling (#25) * Add author name in README.md * orf calling updted to run from command line Co-authored-by: gsheynkman <[email protected]> * Adds nextflow files and folders based on nf-core template (#26) * Adds nf-core template for nextflow pips * Cleans up template main.nf and adds swag cli message * Updates nextflow.config * Adds Dockerfile and env yaml updates * Removes redundant files from assets * Deleted nf schema json * Removes redundant configs * Updates README with template structure * Updates docs/ * Updates repo name in changelog * Updates template test.config * Adds bin folder and template wrapper R script * Adds pbccs in env.yml * Changes the location of pipeline info, logs * Adds .github folder * Removes redundant files from GH actions * Removes AWS tests * Adds misspelling test * Removes linting.yml * Removes igenomes config * Adds tentative LICENSE (MIT) * Adds nudge for asking help via GH issues * added pull scripts from the zenodo site * weighted protein inference * fixes * remove script to hopefully avoid merge conflict.. * update mzLib * require equal long read weight for indistinguishable proteins * add contrib * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * update main readme with author names (#38) * update README contributions * new readme * fix minor errors in readme (#40) * update README contributions * new readme * fix readme errors * excel compatible tsv by default * accept thermo license by default * Updated READMEs, uploaded scripts for isoform mapping, protein clustering. (#41) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * delete files that shouldn't be part of the previous commit, old scripts accidentally put in DatabaseAnnotation * updated contributions (#44) * Attempt to create a container for blast mapping process within nextflow. (#48) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * adding cpat and transdecoder containers (#36) * added pull scripts from the zenodo site * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Added commands to run CPAT. 'output' directory to .gitignore. (#53) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Add nextflow-related files, sundries. (#55) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Adding Simi's transcriptomic and peptide analysis scripts. (#56) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Gloria adding Simi's transcriptome analysis and peptide analysis scripts. * argparse modification (#57) * adds lr_orfcalling.nf and lr_orfcalling_nextflow.config in the module LR_ORFCalling (#59) * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * created local lr_orfcalling.nf and _nextflow.config to aid in local testing and debugging before final merge into pipeline * adding main.nf and nextflow.config * Protein Inference Analysis Module Custom Script (#64) * Adds Rachel Miller to the author names in the README * custom script for the comparison of protein group output from MetaMorpheus searches using different protein database reference models * Add files via upload Update of peptide analysis jupyter notebook script * Need to merge with latest dev (disregarding differences in dev_gloria, which are outdated) (#67) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Gloria adding Simi's transcriptome analysis and peptide analysis scripts. * Update orf_calling.py Removed a line to match spacing with the py file in dev. * Convert jupyter notebook into python * ORF Calling - bug fix (#70) * argparse modification * small import bug fix Co-authored-by: gsheynkman <[email protected]> * Update README.md (#65) * Update README.md * Update README.md spelling fixes * Update README.md * ORF Filtering bug fixes and RefineDB (#71) * argparse modification * small import bug fix * fixed bugs in orf_filter. module for refining db * refine orf working Co-authored-by: gsheynkman <[email protected]> * Adds Dockerfile, environment.yml for SQANTI3 (#72) * Adds Dockerfile, environment.yml for SQANTI3 * Improves container files Co-authored-by: EC2 Default User <[email protected]> * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * Updated peptide analysis file (#66) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Add files via upload Update of peptide analysis jupyter notebook script * Convert jupyter notebook into python * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * 6frm readme (#45) * Add initial code to extract and cluster pacbio protein sequences, based on input from LR_ORFCalling * Started code for protein group mapping * add toy tables for the protein inference mapping * edited 6frm translate readme * delete mock files for protein inference (protein group) comparisons. Rachel and Kyndalanne have continued to work on this and these may be outdated. Co-authored-by: Robert Millikin <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> * Protein Inference (#74) * Separate module for greedy protein inference * protein_inference bug fix * added rescue to greedy algorithm * connected peptides changed to set * small bug fix. cleaned up notebook * Removed unnecessary files from Transcriptome Module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module (#75) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Add files via upload Update of peptide analysis jupyter notebook script * Convert jupyter notebook into python * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * Removed unnecessary files from Transcriptome Module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Simi and Gloria - Update referencetable, transcriptome, and peptide modules (#78) * Files in progress to create three modules: ReferenceTables, TranscriptomeAnalysis, PeptideAnalysis. Also, debugged orf_calling.py, found that minus strand ORFs not included. * Prepared a script that makes reference tables * Updated Transcriptomic Script * Updated Transcriptomic Script (#77) Co-authored-by: kyuubi430 <[email protected]> * Remove files for making three modules with simi. * Cleaned up referencetable module, Simi to edit. * Modified Reference Tables Script * Deleted plots. * Simi and Gloria finalized the prepare_reference_tables. Works on commandline. Correct outputs to results/PG_ReferenceTables. * Small edits to peptide_analysis, not done, push to Simi. * Modified the names out output files from Prepare Reference Tabe script * Changed file names in reference tables script and modified the transcriptome summary * Delete unneeded files in transcriptome summary module. * Finalized ReferenceTables. tested Transcriptome Summary. Started modifying the PeptideAnalysis. * Made the transcriptome summary script command line executable * Made the peptide analysis script command line runnable * In process of modifying MMprocessing script * Move scripts between TranscriptomeSummary and PeptideAnalysis modules. Code related to MM peptide/protein processing will now be exclusively in PeptideAnalysis. * Added fasta/tsv and the results directory to gitignore * Delete jurkat_orf_refined.fasta Don't want to include *fasta in pull request. * Delete genes_in_refined.tsv Don't want to include *tsv output file in PR. Added *tsv to gitignore, so shouldn't upload in future PR. Co-authored-by: kyuubi430 <[email protected]> * Adds modules nextflow pseudocode (#79) * Adds nf-core template for nextflow pips * Cleans up template main.nf and adds swag cli message * Updates nextflow.config * Adds Dockerfile and env yaml updates * Removes redundant files from assets * Deleted nf schema json * Removes redundant configs * Updates README with template structure * Updates docs/ * Updates repo name in changelog * Updates template test.config * Adds bin folder and template wrapper R script * Adds pbccs in env.yml * Changes the location of pipeline info, logs * Adds .github folder * Removes redendant files from GH actions * Updates CONTRIBUTING.md * Updates ISSUE_TEMPLATE * Update PULL_REQUEST_TEMPLATE.md * Removes AWS tests * Adds misspelling test * Removes linting.yml * Corrects typo * Removes igenomes config * Fixes typos caught by review-dog * Adds tentative LICENSE * Adds environment.yml with pandas, numpy, biopython * Adds CCS process * Adds pbbam (required for ccs --chunk subsequent routine) * Adds pbindex, ccs processes (w/ parallel --chunks) * Removes redundant bai (pbi is needed) * Adds temp process mock ccs and flag for testing * Deletes commented out section To respect the rule, "we do not choose to modify cod ebehaviour by commenting in and out code chunks", * Makes the section note more informative * Dev rmmiller protein inference (#83) * Adds Rachel Miller to the author names in the README * custom script for the comparison of protein group output from MetaMorpheus searches using different protein database reference models * Make protein inference analysis script command line executable * spelling fixes * Update PI_proteinInferenceAnalysis.py fix merge conflicts * Adds nextflow referencetable, notes to SQANTI module. (#88) * Initiated files for nextflowifying reference-table module. * Add nextflow code for reference table module. Successfully run on Lifebit/CloudOS. * Rename transcript script. Add notes on requirements and commands to run SQANTI. * Adds nextflow refined db (#80) * Moves refine_orfs.py * Restores tsv vs csv in refine_orfs.py * Adds Nextflow files for refined db generation * Refactor Dockerfile to eliminate duplication of env name * Updates README.md in the modules/LR_ORFCalling subdirectory and lr_orfcalling.nf and lr_orfcalling_nextflow.config (#63) * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * created local lr_orfcalling.nf and _nextflow.config to aid in local testing and debugging before final merge into pipeline * adding main.nf and nextflow.config * added to README.md instructions for executing nextflow within a jupyter notebook for debugging * Update README.md * Update README.md * Updates ORF calling Nextflow files (#73) * Updates ORF calling Nextflow snippet * Deletes redundant global container definition * Removes superfluous new line * Clean up of comments * Updates channel syntax to simplify to 1 line * Adds TransDecoder in log.info summary * Adds nextflow_run.sh with commands, expected exits * Improves code readability, adds file exists check Co-authored-by: EC2 Default User <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: EC2 Default User <[email protected]> Co-authored-by: bj8th <[email protected]> * Clean up peptide analysis module. * Remove README * Add nextflow io (#100) * added input output to readmes and modified to run via main * refine database readme * pull request changes made * Clean up peptideanalysismodule (#99) * Clean up peptide analysis module. * Remove README * Add module to make gencode protein database. * Add module to make PacBio CDS. * Bj8th readme (#102) * added readme information to several modules. updated modules to run from command line * added source modules Co-authored-by: kyuubi430 <[email protected]> Co-authored-by: kyuubi430 <[email protected]> Co-authored-by: rob <[email protected]> Co-authored-by: trishorts <[email protected]> Co-authored-by: Michael Shortreed <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: rmmiller22 <[email protected]> Co-authored-by: Anne Deslattes Mays <[email protected]> Co-authored-by: bj8th <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: EC2 Default User <[email protected]>
bj8th
added a commit
that referenced
this pull request
Dec 14, 2020
* Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Adds Author Name in README (#15) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * add long read info basics * gui app manifest gitignore fix * Adds @trishorts name in README.md (#18) * add author name to readme.md * add one line to refresh commit * add author name Co-authored-by: Michael Shortreed <[email protected]> Co-authored-by: cgpu <[email protected]> * Adds @gsheynkman name to README.md (#16) * Added authorname in README Co-authored-by: cgpu <[email protected]> * Adds Rachel Miller to the author names in the README (#14) * Adds Rachel Miller to the author names in the README * Minor typo Co-authored-by: cgpu <[email protected]> * added author and ORCID (#12) Co-authored-by: cgpu <[email protected]> * Refined database orig code (#29) * Add initial code to extract and cluster pacbio protein sequences, based on input from LR_ORFCalling * aggregation of FL and CPM by cluster Co-authored-by: Robert Millikin <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> * Bj8th orf calling (#25) * Add author name in README.md * orf calling updted to run from command line Co-authored-by: gsheynkman <[email protected]> * Adds nextflow files and folders based on nf-core template (#26) * Adds nf-core template for nextflow pips * Cleans up template main.nf and adds swag cli message * Updates nextflow.config * Adds Dockerfile and env yaml updates * Removes redundant files from assets * Deleted nf schema json * Removes redundant configs * Updates README with template structure * Updates docs/ * Updates repo name in changelog * Updates template test.config * Adds bin folder and template wrapper R script * Adds pbccs in env.yml * Changes the location of pipeline info, logs * Adds .github folder * Removes redundant files from GH actions * Removes AWS tests * Adds misspelling test * Removes linting.yml * Removes igenomes config * Adds tentative LICENSE (MIT) * Adds nudge for asking help via GH issues * added pull scripts from the zenodo site * weighted protein inference * fixes * remove script to hopefully avoid merge conflict.. * update mzLib * require equal long read weight for indistinguishable proteins * add contrib * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * update main readme with author names (#38) * update README contributions * new readme * fix minor errors in readme (#40) * update README contributions * new readme * fix readme errors * excel compatible tsv by default * accept thermo license by default * Updated READMEs, uploaded scripts for isoform mapping, protein clustering. (#41) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * delete files that shouldn't be part of the previous commit, old scripts accidentally put in DatabaseAnnotation * updated contributions (#44) * Attempt to create a container for blast mapping process within nextflow. (#48) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * adding cpat and transdecoder containers (#36) * added pull scripts from the zenodo site * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Added commands to run CPAT. 'output' directory to .gitignore. (#53) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Add nextflow-related files, sundries. (#55) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Adding Simi's transcriptomic and peptide analysis scripts. (#56) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Gloria adding Simi's transcriptome analysis and peptide analysis scripts. * argparse modification (#57) * adds lr_orfcalling.nf and lr_orfcalling_nextflow.config in the module LR_ORFCalling (#59) * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * created local lr_orfcalling.nf and _nextflow.config to aid in local testing and debugging before final merge into pipeline * adding main.nf and nextflow.config * Protein Inference Analysis Module Custom Script (#64) * Adds Rachel Miller to the author names in the README * custom script for the comparison of protein group output from MetaMorpheus searches using different protein database reference models * Add files via upload Update of peptide analysis jupyter notebook script * Need to merge with latest dev (disregarding differences in dev_gloria, which are outdated) (#67) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Gloria adding Simi's transcriptome analysis and peptide analysis scripts. * Update orf_calling.py Removed a line to match spacing with the py file in dev. * Convert jupyter notebook into python * ORF Calling - bug fix (#70) * argparse modification * small import bug fix Co-authored-by: gsheynkman <[email protected]> * Update README.md (#65) * Update README.md * Update README.md spelling fixes * Update README.md * ORF Filtering bug fixes and RefineDB (#71) * argparse modification * small import bug fix * fixed bugs in orf_filter. module for refining db * refine orf working Co-authored-by: gsheynkman <[email protected]> * Adds Dockerfile, environment.yml for SQANTI3 (#72) * Adds Dockerfile, environment.yml for SQANTI3 * Improves container files Co-authored-by: EC2 Default User <[email protected]> * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * Updated peptide analysis file (#66) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Add files via upload Update of peptide analysis jupyter notebook script * Convert jupyter notebook into python * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * 6frm readme (#45) * Add initial code to extract and cluster pacbio protein sequences, based on input from LR_ORFCalling * Started code for protein group mapping * add toy tables for the protein inference mapping * edited 6frm translate readme * delete mock files for protein inference (protein group) comparisons. Rachel and Kyndalanne have continued to work on this and these may be outdated. Co-authored-by: Robert Millikin <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> * Protein Inference (#74) * Separate module for greedy protein inference * protein_inference bug fix * added rescue to greedy algorithm * connected peptides changed to set * small bug fix. cleaned up notebook * Removed unnecessary files from Transcriptome Module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module (#75) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Add files via upload Update of peptide analysis jupyter notebook script * Convert jupyter notebook into python * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * Removed unnecessary files from Transcriptome Module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Simi and Gloria - Update referencetable, transcriptome, and peptide modules (#78) * Files in progress to create three modules: ReferenceTables, TranscriptomeAnalysis, PeptideAnalysis. Also, debugged orf_calling.py, found that minus strand ORFs not included. * Prepared a script that makes reference tables * Updated Transcriptomic Script * Updated Transcriptomic Script (#77) Co-authored-by: kyuubi430 <[email protected]> * Remove files for making three modules with simi. * Cleaned up referencetable module, Simi to edit. * Modified Reference Tables Script * Deleted plots. * Simi and Gloria finalized the prepare_reference_tables. Works on commandline. Correct outputs to results/PG_ReferenceTables. * Small edits to peptide_analysis, not done, push to Simi. * Modified the names out output files from Prepare Reference Tabe script * Changed file names in reference tables script and modified the transcriptome summary * Delete unneeded files in transcriptome summary module. * Finalized ReferenceTables. tested Transcriptome Summary. Started modifying the PeptideAnalysis. * Made the transcriptome summary script command line executable * Made the peptide analysis script command line runnable * In process of modifying MMprocessing script * Move scripts between TranscriptomeSummary and PeptideAnalysis modules. Code related to MM peptide/protein processing will now be exclusively in PeptideAnalysis. * Added fasta/tsv and the results directory to gitignore * Delete jurkat_orf_refined.fasta Don't want to include *fasta in pull request. * Delete genes_in_refined.tsv Don't want to include *tsv output file in PR. Added *tsv to gitignore, so shouldn't upload in future PR. Co-authored-by: kyuubi430 <[email protected]> * Adds modules nextflow pseudocode (#79) * Adds nf-core template for nextflow pips * Cleans up template main.nf and adds swag cli message * Updates nextflow.config * Adds Dockerfile and env yaml updates * Removes redundant files from assets * Deleted nf schema json * Removes redundant configs * Updates README with template structure * Updates docs/ * Updates repo name in changelog * Updates template test.config * Adds bin folder and template wrapper R script * Adds pbccs in env.yml * Changes the location of pipeline info, logs * Adds .github folder * Removes redendant files from GH actions * Updates CONTRIBUTING.md * Updates ISSUE_TEMPLATE * Update PULL_REQUEST_TEMPLATE.md * Removes AWS tests * Adds misspelling test * Removes linting.yml * Corrects typo * Removes igenomes config * Fixes typos caught by review-dog * Adds tentative LICENSE * Adds environment.yml with pandas, numpy, biopython * Adds CCS process * Adds pbbam (required for ccs --chunk subsequent routine) * Adds pbindex, ccs processes (w/ parallel --chunks) * Removes redundant bai (pbi is needed) * Adds temp process mock ccs and flag for testing * Deletes commented out section To respect the rule, "we do not choose to modify cod ebehaviour by commenting in and out code chunks", * Makes the section note more informative * Dev rmmiller protein inference (#83) * Adds Rachel Miller to the author names in the README * custom script for the comparison of protein group output from MetaMorpheus searches using different protein database reference models * Make protein inference analysis script command line executable * spelling fixes * Update PI_proteinInferenceAnalysis.py fix merge conflicts * rescue algorithm implemented * eliminate added conflict files * config file remove * spelling fix Co-authored-by: kyuubi430 <[email protected]> Co-authored-by: kyuubi430 <[email protected]> Co-authored-by: rob <[email protected]> Co-authored-by: trishorts <[email protected]> Co-authored-by: Michael Shortreed <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: gsheynkman <[email protected]> Co-authored-by: Anne Deslattes Mays <[email protected]> Co-authored-by: bj8th <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: EC2 Default User <[email protected]>
bj8th
added a commit
that referenced
this pull request
Dec 28, 2020
* Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Adds Author Name in README (#15) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * add long read info basics * gui app manifest gitignore fix * Adds @trishorts name in README.md (#18) * add author name to readme.md * add one line to refresh commit * add author name Co-authored-by: Michael Shortreed <[email protected]> Co-authored-by: cgpu <[email protected]> * Adds @gsheynkman name to README.md (#16) * Added authorname in README Co-authored-by: cgpu <[email protected]> * Adds Rachel Miller to the author names in the README (#14) * Adds Rachel Miller to the author names in the README * Minor typo Co-authored-by: cgpu <[email protected]> * added author and ORCID (#12) Co-authored-by: cgpu <[email protected]> * Refined database orig code (#29) * Add initial code to extract and cluster pacbio protein sequences, based on input from LR_ORFCalling * aggregation of FL and CPM by cluster Co-authored-by: Robert Millikin <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> * Bj8th orf calling (#25) * Add author name in README.md * orf calling updted to run from command line Co-authored-by: gsheynkman <[email protected]> * Adds nextflow files and folders based on nf-core template (#26) * Adds nf-core template for nextflow pips * Cleans up template main.nf and adds swag cli message * Updates nextflow.config * Adds Dockerfile and env yaml updates * Removes redundant files from assets * Deleted nf schema json * Removes redundant configs * Updates README with template structure * Updates docs/ * Updates repo name in changelog * Updates template test.config * Adds bin folder and template wrapper R script * Adds pbccs in env.yml * Changes the location of pipeline info, logs * Adds .github folder * Removes redundant files from GH actions * Removes AWS tests * Adds misspelling test * Removes linting.yml * Removes igenomes config * Adds tentative LICENSE (MIT) * Adds nudge for asking help via GH issues * added pull scripts from the zenodo site * weighted protein inference * fixes * remove script to hopefully avoid merge conflict.. * update mzLib * require equal long read weight for indistinguishable proteins * add contrib * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * update main readme with author names (#38) * update README contributions * new readme * fix minor errors in readme (#40) * update README contributions * new readme * fix readme errors * excel compatible tsv by default * accept thermo license by default * Updated READMEs, uploaded scripts for isoform mapping, protein clustering. (#41) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * delete files that shouldn't be part of the previous commit, old scripts accidentally put in DatabaseAnnotation * updated contributions (#44) * Attempt to create a container for blast mapping process within nextflow. (#48) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * adding cpat and transdecoder containers (#36) * added pull scripts from the zenodo site * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Added commands to run CPAT. 'output' directory to .gitignore. (#53) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Add nextflow-related files, sundries. (#55) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Adding Simi's transcriptomic and peptide analysis scripts. (#56) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Gloria adding Simi's transcriptome analysis and peptide analysis scripts. * argparse modification (#57) * adds lr_orfcalling.nf and lr_orfcalling_nextflow.config in the module LR_ORFCalling (#59) * adding cpat and transdecoder containers * adding the empty data directory with README.md explaining why it is empty on github * github actions caught my spelling error * left out in front of the conda commands for both these containers * added debugged containers * moved test.config to conf/executor/test.config * fixed syntax error executor -> executors * created local lr_orfcalling.nf and _nextflow.config to aid in local testing and debugging before final merge into pipeline * adding main.nf and nextflow.config * Protein Inference Analysis Module Custom Script (#64) * Adds Rachel Miller to the author names in the README * custom script for the comparison of protein group output from MetaMorpheus searches using different protein database reference models * Add files via upload Update of peptide analysis jupyter notebook script * Need to merge with latest dev (disregarding differences in dev_gloria, which are outdated) (#67) * Updated various readmes. Uploaded scripts for isoform mappings, protein clustering, etc. * Add scripts that run blast and parse blast results to find at-length matches between isoforms. Need to combine with Anne's pipeline. * add scripts for blast mapping between protein databases * Attempt to create nextflow container to do blast searching for isoform accession mapping * correct spelling error * Made amendments to orf_calling.py. * CPAT commands. Added output directory to gitignore. Outupt directly to hold intermediate datafiles. * Gloria adding Simi's transcriptome analysis and peptide analysis scripts. * Update orf_calling.py Removed a line to match spacing with the py file in dev. * Convert jupyter notebook into python * ORF Calling - bug fix (#70) * argparse modification * small import bug fix Co-authored-by: gsheynkman <[email protected]> * Update README.md (#65) * Update README.md * Update README.md spelling fixes * Update README.md * ORF Filtering bug fixes and RefineDB (#71) * argparse modification * small import bug fix * fixed bugs in orf_filter. module for refining db * refine orf working Co-authored-by: gsheynkman <[email protected]> * Adds Dockerfile, environment.yml for SQANTI3 (#72) * Adds Dockerfile, environment.yml for SQANTI3 * Improves container files Co-authored-by: EC2 Default User <[email protected]> * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * Updated peptide analysis file (#66) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Add files via upload Update of peptide analysis jupyter notebook script * Convert jupyter notebook into python * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * 6frm readme (#45) * Add initial code to extract and cluster pacbio protein sequences, based on input from LR_ORFCalling * Started code for protein group mapping * add toy tables for the protein inference mapping * edited 6frm translate readme * delete mock files for protein inference (protein group) comparisons. Rachel and Kyndalanne have continued to work on this and these may be outdated. Co-authored-by: Robert Millikin <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> * Protein Inference (#74) * Separate module for greedy protein inference * protein_inference bug fix * added rescue to greedy algorithm * connected peptides changed to set * small bug fix. cleaned up notebook * Removed unnecessary files from Transcriptome Module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module (#75) * Adds author name in README.md * Adds author name in README.md * Deletes temp file * Adds author name in README.md * Modified README.md File in LR_TranscriptomeSummary * Add files via upload This adds the genomic data compilation and comparison jupyter notebook script and adds several custom module dependencies. * Update README.md * Updated version of previous files with less typos * Delete Transcriptomic_Proteomic_Comparison.ipynb * Delete m_MMprocess.py * Delete m_gen_maps.py * Delete m_make_gene_length_table.py * Delete m_sqantitable.py * Delete m_squantitable.py * Updated version with less typos * Update README.md * Preliminary module for analyzing peptide space * Add files via upload Update of peptide analysis jupyter notebook script * Convert jupyter notebook into python * Updated peptide_analysis script for review and added required files/tables * Update peptide_analysis.py * Updated .gitignore with a local data file * Updated peptide_analysis.py to include new path info * Delete gene_based_info.tsv * Delete trans_to_gene.tsv * Removed unnecessary files from Transcriptome Module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Removed unnecessary files from Transcriptome module * Simi and Gloria - Update referencetable, transcriptome, and peptide modules (#78) * Files in progress to create three modules: ReferenceTables, TranscriptomeAnalysis, PeptideAnalysis. Also, debugged orf_calling.py, found that minus strand ORFs not included. * Prepared a script that makes reference tables * Updated Transcriptomic Script * Updated Transcriptomic Script (#77) Co-authored-by: kyuubi430 <[email protected]> * Remove files for making three modules with simi. * Cleaned up referencetable module, Simi to edit. * Modified Reference Tables Script * Deleted plots. * Simi and Gloria finalized the prepare_reference_tables. Works on commandline. Correct outputs to results/PG_ReferenceTables. * Small edits to peptide_analysis, not done, push to Simi. * Modified the names out output files from Prepare Reference Tabe script * Changed file names in reference tables script and modified the transcriptome summary * Delete unneeded files in transcriptome summary module. * Finalized ReferenceTables. tested Transcriptome Summary. Started modifying the PeptideAnalysis. * Made the transcriptome summary script command line executable * Made the peptide analysis script command line runnable * In process of modifying MMprocessing script * Move scripts between TranscriptomeSummary and PeptideAnalysis modules. Code related to MM peptide/protein processing will now be exclusively in PeptideAnalysis. * Added fasta/tsv and the results directory to gitignore * Delete jurkat_orf_refined.fasta Don't want to include *fasta in pull request. * Delete genes_in_refined.tsv Don't want to include *tsv output file in PR. Added *tsv to gitignore, so shouldn't upload in future PR. Co-authored-by: kyuubi430 <[email protected]> * Adds modules nextflow pseudocode (#79) * Adds nf-core template for nextflow pips * Cleans up template main.nf and adds swag cli message * Updates nextflow.config * Adds Dockerfile and env yaml updates * Removes redundant files from assets * Deleted nf schema json * Removes redundant configs * Updates README with template structure * Updates docs/ * Updates repo name in changelog * Updates template test.config * Adds bin folder and template wrapper R script * Adds pbccs in env.yml * Changes the location of pipeline info, logs * Adds .github folder * Removes redendant files from GH actions * Updates CONTRIBUTING.md * Updates ISSUE_TEMPLATE * Update PULL_REQUEST_TEMPLATE.md * Removes AWS tests * Adds misspelling test * Removes linting.yml * Corrects typo * Removes igenomes config * Fixes typos caught by review-dog * Adds tentative LICENSE * Adds environment.yml with pandas, numpy, biopython * Adds CCS process * Adds pbbam (required for ccs --chunk subsequent routine) * Adds pbindex, ccs processes (w/ parallel --chunks) * Removes redundant bai (pbi is needed) * Adds temp process mock ccs and flag for testing * Deletes commented out section To respect the rule, "we do not choose to modify cod ebehaviour by commenting in and out code chunks", * Makes the section note more informative * Dev rmmiller protein inference (#83) * Adds Rachel Miller to the author names in the README * custom script for the comparison of protein group output from MetaMorpheus searches using different protein database reference models * Make protein inference analysis script command line executable * spelling fixes * Update PI_proteinInferenceAnalysis.py fix merge conflicts * rescue algorithm implemented * eliminate added conflict files * config file remove * spelling fix * Update mzLib version- includes database parsing changes * Test Update Co-authored-by: kyuubi430 <[email protected]> Co-authored-by: kyuubi430 <[email protected]> Co-authored-by: rob <[email protected]> Co-authored-by: trishorts <[email protected]> Co-authored-by: Michael Shortreed <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: gsheynkman <[email protected]> Co-authored-by: Anne Deslattes Mays <[email protected]> Co-authored-by: bj8th <[email protected]> Co-authored-by: Gloria Sheynkman <[email protected]> Co-authored-by: cgpu <[email protected]> Co-authored-by: EC2 Default User <[email protected]>
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This PR adds the nextflow specific files in the root of the repo. The files were auto-generated (using the
nf-core createcommand) and editted to simplify and remove boilerplate.