Releases: friendsofstrandseq/mosaicatcher-pipeline
Releases · friendsofstrandseq/mosaicatcher-pipeline
1.8.2
Features
- Genecore mode
Bugs
- Change env to solve pyyaml issue in run summary
@weber8thomas in #16
Full Changelog: 1.8.1...1.8.2
Contributors
weber8thomas
Assets 2
1.8.1
release_please.yaml update
1.7.0
Commits
- b243341: Add new rules for the different human assemblies (hg19, hg38, T2T) (Thomas Weber) #11
- 94f0f1a: Solve small issue on handle_input_data.py (Thomas Weber)
- 5e61cec: Docs and local profiles (Thomas Weber) #10
- 4a2fe72: Docs and local profiles (Thomas Weber) #10
- 7ae1693: Docs and local profiles (Thomas Weber) #10
- 356aed4: Docs and local profiles (Thomas Weber) #10
- ab8c230: Docs and local profiles (Thomas Weber) #10
- b2db31c: Docs and local profiles (Thomas Weber) #10
- 001f7cd: Many changes related to ref genomes (Thomas Weber) #11
- b224348: Major update: (Thomas Weber) #11
- 0b99279: Major update: (Thomas Weber) #11
- 6ab62f2: Major update: (Thomas Weber) #11
- def323b: Major update: (Thomas Weber) #11
- 36f5928: Major update: (Thomas Weber) #11
- 8d3de43: Major update: (Thomas Weber) #11
- feb013f: Major update: (Thomas Weber) #11
- 39c385a: Major update: (Thomas Weber) #11
- cd31c86: Major update: (Thomas Weber) #11
- f989c08: Major update: (Thomas Weber) #11
- 3732ad0: Major update: (Thomas Weber) #11
- b69db6e: Detect Single/Paired end sample (Thomas Weber) #11
- 107c594: Detect Single/Paired end sample (Thomas Weber) #11
- d0aff87: Detect Single/Paired end sample (Thomas Weber) #11
- 10eaf25: Detect Single/Paired end sample (Thomas Weber) #11
- 2351c24: Detect Single/Paired end sample (Thomas Weber) #11
- c6c9c1d: Detect Single/Paired end sample (Thomas Weber) #11
- 2c93e98: Detect Single/Paired end sample (Thomas Weber) #11
- 72d25b4: Detect Single/Paired end sample (Thomas Weber) #11
- f844a73: Solve paired_end issue: automatic detection of single/paired end in BAM files (Thomas Weber) #11
- 19e75ed: Solve paired_end issue: automatic detection of single/paired end in BAM files (Thomas Weber) #11
- aee7334: Solve paired_end issue: automatic detection of single/paired end in BAM files (Thomas Weber) #11
- 6d27e7a: Docs (Thomas Weber) #11
- 3f3d916: Linting & Formatting (Thomas Weber) #11
- b86d08c: Linting & Formatting (Thomas Weber) #11
- 5aee279: (Re-)Added normalization parts (Thomas Weber) #11
- 299878f: (Re-)Added normalization parts (Thomas Weber) #11
- 6b25be0: (Re-)Added normalization parts (Thomas Weber) #11
- 5b5b7a6: (Re-)Added normalization parts (Thomas Weber) #11
- 87703ae: (Re-)Added normalization parts (Thomas Weber) #11
- c1f41ce: (Re-)Added normalization parts (Thomas Weber) #11
- 07fca57: (Re-)Added normalization parts (Thomas Weber) #11
- 7333e8d: (Re-)Added normalization parts (Thomas Weber) #11
- 548b905: (Re-)Added normalization parts (Thomas Weber) #11
- 30763d0: Merge branch 'master' into ref_genomes (Thomas Weber) #11
- 1c62749: README issue (Thomas Weber)
- e6a3e76: README issue (Thomas Weber)
- 81f5f6a: README issue (Thomas Weber)
- 5aeae65: README issue (Thomas Weber)
- b8afff5: Corrections (Thomas Weber)
- 4edd604: Snakemake log tests (Thomas Weber) #12
- 6940e8e: Corrections (Thomas Weber)
- 770bfd9: Solve small issues (strandphaser single-cell haps comparison) (Thomas Weber)
- 302f7b5: Solve stringent/lenient issue (filter = TRUE/FALSE) (Thomas Weber)
- cb9a659: Merge branch 'master' into dev (Thomas Weber) #12
- b82ba2b: Solve multi-sample issue (Thomas Weber) #12
- 1e5d12c: Solve multi-sample issue (Thomas Weber) #12
- 6f5c413: Cleaning (Thomas Weber) #12
- b18b6b3: Solve multi-sample issue (Thomas Weber) #12
- 8b2d291: Solve multi-sample issue (Thomas Weber) #12
- 5a32bed: Solve multi-sample issue (Thomas Weber) #12
- edb9b4b: Test debug (Thomas Weber) #12
- 07050de: Test debug (Thomas Weber) #12
- fa6e6de: Test debug (Thomas Weber) #12
- 8065726: Test debug (Thomas Weber) #12
- 92469f9: Test debug (Thomas Weber) #12
- b16a3a2: Test debug (Thomas Weber) #12
- 7c51082: Test debug (Thomas Weber) #12
- b28ec25: Test debug (Thomas Weber) #12
- 3e3a408: Test debug (Thomas Weber) #12
- f1ede48: Test debug (Thomas Weber) #12
- e3239eb: Test debug (Thomas Weber) #12
- 3d43435: Test debug clustering (Thomas Weber) #12
- a113ebf: Test debug ploidy (Thomas Weber) #12
- 3e0fcf8: Test debug stats-merged (Thomas Weber) #12
- 3da0b91: Test debug run-summary (Thomas Weber) #12
- 7b54582: Test debug complex (Thomas Weber) #12
- 6ea1658: Test debug complex2 (Thomas Weber) #12
- 001160e: Test debug fastq (Thomas Weber) #12
- 071ae2e: Test debug ; change envs (Thomas Weber) #12
- 5d4eab4: Test debug ; change envs (Thomas Weber) #12
- 7c88a5a: Test debug ; change envs (Thomas Weber) #12
- 4a07f1a: Test debug (Thomas Weber) #12
- df08a4b: Test debug (Thomas Weber) #12
- 236b059: Test debug (Thomas Weber) #12
- 928ad89: From chr21 to chr17 to solve issues (Thomas Weber) [#12](https://github.com/friendsofstrandseq/mosaicatcher-pipeline/pull...
1.6.0
Major release
- New parameter to load data preprocessing module ashleys-qc-pipeline
- Automatic detection of low-quality cells and dynamic modification of the DAG through checkpoint rule filter_bad_cells
- snakemake-workflow-catalog compliant format
Commits
- 438dd97: Formatting - Major update (Thomas Weber) #7
- 9c363e0: Snakefmt (Thomas Weber) #7
- 44e7998: Dockerfile change (Thomas Weber) #7
- 1df311d: Change font family in qc.R script (Thomas Weber) #7
- b867a37: Snakemake github action test (Thomas Weber) #7
- 5437d25: Snakemake github action test (Thomas Weber) #7
- 2aae10e: Docs & Snakemake github action test (Thomas Weber) #7
- bf65379: Dockerfile update (Thomas Weber)
- 557ae48: GitHub actions update (Thomas Weber)
- 0089419: Regenotyping parameter error correction (Thomas Weber)
- bcefa00: new rule: filter_bad_cells_from_mosaic_count (Thomas Weber) #7
- 55d9a3f: Cleaning, updating slurm profile (Thomas Weber)
- 0f375a9: Add issue template (Thomas Weber)
- b52d533: Docs, config & minor changes (Thomas Weber)
- e6287f6: Major update (Thomas Weber) #7
- 6340ae6: Small changes to fix GitHub issues actions (Thomas Weber) #7
- c69a7da: Dockerfile_complete created (Thomas Weber) #7
- 830ffb7: Update docker GitHub actions (Thomas Weber) #7
- f05c054: Git update (Thomas Weber) #7
- 846b76a: Update docker GitHub actions (Thomas Weber) #7
- 2a58be4: combine_strandphaser_output issue: solving attempt (1) (Thomas Weber) #7
- 0329c77: combine_strandphaser_output issue: solving attempt (1) (Thomas Weber) #7
- e371e7a: combine_strandphaser_output issue: solving attempt (2) (Thomas Weber) #7
- f65c80c: Re-enabled divide PDF in final targets (Thomas Weber) #7
- c69c62e: Enabled debug / verbose in GitHub actions (ashleys module imported) (Thomas Weber) #7
- 8562a5b: Snakefmt + lint (Thomas Weber) #7
- 01d058a: Update GitHub actions workflows files (Thomas Weber) #9
- 676469e: Update README.md (Thomas Weber)
What's Changed
- New release by @weber8thomas in #7
- Update GitHub actions workflows files by @weber8thomas in #9
Full Changelog: 1.5...1.6.0
Contributors
weber8thomas
Assets 2
1.5.1-dev
Commits
- 3fc2e47: Test pipeline run in CI CD (Thomas Weber)
- 6dc119d: Update (Thomas Weber)
- fcb8a41: Update (Thomas Weber)
- d3831b8: Test git (Thomas Weber)
- cae5e87: Test git (Thomas Weber)
- c85503d: Test git merge (Thomas Weber)
- 16a583b: Test git merge (Thomas Weber)
- 8d05225: Update README.md (Thomas Weber)
- 99b44f9: Update README.md (Thomas Weber)
- 30eaeec: Update README.md\nUpdate .gitignore (Thomas Weber)
- 480c9ef: Update README.md\nUpdate .gitignore (Thomas Weber)
- 8a4a3a7: Update README.md\nUpdate .gitignore\nImplemented remote file pull using zenodo (Thomas Weber)
- dee7f13: Update README.md\nUpdate .gitignore\nImplemented remote file pull using zenodo (Thomas Weber)
- 7582aba: Update README.md\nUpdate .gitignore\nImplemented remote file pull using zenodo (Thomas Weber)
- b1065fc: Update README.md\nUpdate .gitignore\nImplemented remote file pull using zenodo (Thomas Weber)
- b721e22: Update README.md\nUpdate .gitignore\nImplemented remote file pull using zenodo (Thomas Weber)
- ad5d0a4: Update README.md\nUpdate .gitignore\nImplemented remote file pull using zenodo (Thomas Weber)
- d9b2b45: Update README.md (Thomas Weber)
- cc24bdb: Update README.md (Thomas Weber)
- e4ef0cc: Update README.md (Thomas Weber)
- b95293d: Update README.md (Thomas Weber)
- 89baae2: Update README.md (Thomas Weber)
- 53b7e68: Update README.md (Thomas Weber)
- cb044fa: Commit to master (Thomas Weber)
- d8f428d: Commit to master (Thomas Weber)
- 98eaaaf: Cleaning master (Thomas Weber)
- 12e4806: Cleaning master (Thomas Weber)
- b79bfc6: Gitignore issue fixed (Thomas Weber)
- 0274473: Gitignore issue fixed (Thomas Weber)
- 4598141: Gitignore issue fixed (Thomas Weber)
- 60a44fd: Gitignore issue fixed (Thomas Weber)
- c582713: Gitignore issue fixed (Thomas Weber)
- 572bc21: Gitignore issue fixed (Thomas Weber)
- 4c53cf5: Gitignore issue fixed (Thomas Weber)
- e303fb6: Gitignore issue fixed (Thomas Weber)
- e5393d4: Gitignore issue fixed (Thomas Weber)
- 7fb0139: Gitignore issue fixed (Thomas Weber)
- 7c6f2d1: Gitignore issue fixed (Thomas Weber)
- f93a2fc: Gitignore issue fixed (Thomas Weber)
- 89931be: Test local runner (Thomas Weber)
- 71c3eb7: Test local runner (Thomas Weber)
- 1ee159f: Test local runner (Thomas Weber)
- c964082: Test local runner (Thomas Weber)
- b4fb3d7: Config issue fixed (Thomas Weber)
- 2f7ad0f: Config issue fixed (Thomas Weber)
- ce78b15: README.md typo fixed (Thomas Weber)
- 77cbaa0: README.md typo fixed (Thomas Weber)
- 62bfcb1: Merge branch 'dev' of git.embl.de:tweber/mosaicatcher-update into dev (Thomas Weber)
- f759c09: Merge branch 'dev' of git.embl.de:tweber/mosaicatcher-update into dev (Thomas Weber)
- 7046770: Merge remote-tracking branch 'origin/master' into dev (Thomas Weber)
- 4db931f: Merge remote-tracking branch 'origin/master' into dev (Thomas Weber)
- 726eb75: Merge branch 'dev' into 'master' (Thomas Weber)
- 7a2dadc: Merge branch 'dev' into 'master' (Thomas Weber)
- 2be8881: Merge remote-tracking branch 'origin/master' into dev (Thomas Weber)
- 44d3315: Update README.md (Thomas Weber)
- 8933f3e: Cleaning .git folder (Thomas Weber)
- b665282: Cleaning .git folder (Thomas Weber)
- 188ac5e: Cleaning .git folder (Thomas Weber)
- bc8baba: Cleaning .git folder (Thomas Weber)
- d880fa1: Test (Thomas Weber)
- ddb6753: Test (Thomas Weber)
- 7dcdca9: Merge branch 'master' of git.embl.de:tweber/mosaicatcher-update (Thomas Weber)
- ed99371: Merge branch 'master' of git.embl.de:tweber/mosaicatcher-update (Thomas Weber)
- ec1142a: Cleaning (Thomas Weber)
- 339ab35: Cleaning (Thomas Weber)
- 877b2d6: Cleaning (Thomas Weber)
- 6297135: Cleaning (Thomas Weber)
- 3cf2c75: Merge branch 'master' of git.embl.de:tweber/mosaicatcher-update (Thomas Weber)
- ea03cd5: Merge branch 'master' of git.embl.de:tweber/mosaicatcher-update (Thomas Weber)
- c4ebf64: Merge branch 'master' of git.embl.de:tweber/mosaicatcher-update (Thomas Weber)
- 6f06804: Cleaning HEAD tags (Thomas Weber)
- e0dd6c0: Cleaning HEAD tags (Thomas Weber)
- 67c93de: Cleaning HEAD tags (Thomas Weber)
- 1b1978a: Update README.md (Thomas Weber)
- e66fe5e: Update README.md (Thomas Weber)
- f0ea661: Update README.md (Thomas Weber)
- b6a46ff: Removing files (Thomas Weber)
- 5f2ee51: Removing files (Thomas Weber)
- b00ef61: Removing files (Thomas Weber)
- a835f79: Download example & external data (Thomas Weber)
- cce4ea9: Download example & external data (Thomas Weber)
- 128ece9: Download example & external data (Thomas Weber)
- 2981040: Remove SIF LFS-tracked files (Thomas Weber)
- fc27182: Remove SIF LFS-tracked files (Thomas Weber)
- 4e55788: Remove SIF LFS-tracked files (Thomas Weber)
- 1ebf64c: Correct README.md (Thomas Weber)
- 5a5a79a: Correct README.md (Thomas Weber)
- 42721d6: Correct README.md (Thomas Weber)
- ba9bff1: Correct README.md (Thomas Weber)
- 79fd20b: Correct README.md (Thomas Weber)
- 32ef131: Correct README.md (Thomas Weber)
- 673d748: Correct README.md (Thomas Weber)
- d97986a: Correct README.md (Thomas Weber)
- c319851: Correct README.md (Thomas Weber)
- 3f0dc28: Initial commit (Thomas Weber)
- 6c87c33: Initial commit (Thomas Weber)
- 9761966: Initial commit (Thomas Weber)
- 932d252: Correct issue (Thomas Weber)
- 3e13fbe: Correct issue (Thomas Weber)
- 88c57ae: Correct issue (Thomas Weber)
- 5ed61ec: Small correction (Thomas Weber)
- b041473: Small correction (Thomas Weber)
- 183dbb9: Small correction (Thomas Weber)
- d84904a: Correct SMK download BAM example files (Thomas Weber)
- b4de69f: Correct SMK download BAM example files (Thomas Weber)
- dd8bbae: Correct SMK download BAM example files (Thomas Weber)
- 881c661: Update README.md (Thomas Weber)
- c4fb699: Update README.md (Thomas Weber)
- b7e1b46: Update README.md (Thomas Weber)
- a4611b7: Check if SM tag are corresponding to folder name (Thomas Weber)
- f12ab4e: Check if SM tag are corresponding to folder name (Thomas Weber)
- 64bd919: Check if SM tag are corresponding to folder name (Thomas Weber)
- dbaca67: Check if SM tag are corresponding to folder name (Thomas Weber)
- 248f088: Update README.md (Thomas Weber)
- b397c7d: Update README.md (Thomas Weber)
- 986ccab: Update README.md (Thomas Weber)
- 211b2a7: Update README.md (Thomas Weber)
- 1e0116e: Working version on LCL sample (H2NCTAFX2_GM20509B_20s000579-1-1) (Thomas Weber)
- 0dc3b03: Working version on LCL sample (H2NCTAFX2_GM20509B_20s000579-1-1) (Thomas Weber)
- 2053c7f: Working version on LCL sample (H2NCTAFX2_GM20509B_20s000579-1-1) (Thomas Weber)
- b7da62c: Working version on LCL sample (H2NCTAFX2_GM20509B_20s000579-1-1) (Thomas Weber)
- 77cf37d: Update chrxy_analysis.py (Thomas Weber)
- 2a7401f: Update chrxy_analysis.py (Thomas Weber)
- 22ecdc6: Update chrxy_analysis.py (Thomas Weber)
- 0b9dfa9: Update chrxy_analysis.py (Thomas Weber)
- 0108885: HPC Slurm fully functionnal on HGSVC samples (Thomas Weber)
- 12836f2: HPC Slurm fully functionnal on HGSVC samples (Thomas Weber)
- 731000a: HPC Slurm fully functionnal on HGSVC samples (Thomas Weber)
- 5db9d40: HPC Slurm fully functionnal on HGSVC samples (Thomas Weber)
- f6b8937: Merge branch 'master' of git.embl.de:tweber/mosaicatcher-update (Thomas Weber)
- fd341ef: Merge branch 'master' of git.embl.de:tweber/mosaicatcher-update (Thomas Weber)
- d1cfbb1: Merge branch 'master' of git.embl.de:tweber/mosaicatcher-update (Thomas Weber)
- 2fe5f0e: Test commit (Thomas Weber)
- e4d4930: Update README.md (Thomas Weber)
- 5cdc7fc: Update README.md (Thomas Weber)
- 8034980: Update README.md (Thomas Weber)
- 762012e: Correct small issue on Snakefile indentation (Thomas Weber)
- 013fa0e: Documentation & GitHub actions test (Thomas Weber)
- abc6ae4: Update .gitignore (Thomas Weber)
- 4daa46c: Update .gitignore (Thomas Weber)
- e080811: Update README.md (Thomas Weber)
- b22dcbb: Update Usage.md (Thomas Weber)
- c4d0919: Minor update (Thomas Weber)
- 5793936: Minor update (Thomas Weber)
- a505e92: Test snakemake-github-actions (Thomas Weber)
- 1905df0: Test snakemake-github-actions (Thomas Weber)
- ca29ade: Test snakemake-github-actions (Thomas Weber)
- 5dbe10e: Test snakemake-github-actions (Thomas Weber)
- 350cd9b: Test snakemake-github-actions (Thomas Weber)
- 56bf8d8: Test snakemake-github-actions (Thomas Weber)
- 1c54624: Test snakemake-github-actions (Thomas Weber)
- 7bf1f5d: Test snakemake-github-actions (Thomas Weber)
- 7f13437: Test snakemake-github-actions (Thomas Weber)
- 95dd23d: Test snakemake-github-actions (Thomas Weber)
- b6a30a2: Test snakemake-github-actions (Thomas Weber)
- eaaa21e: Test snakemake-github-actions (Thomas Weber)
- 77187c6: Test snakemake-github-actions (Thomas Weber)
- 6269a0c: Test snakemake-github-actions (Thomas Weber)
- d6e97c4: Test snakemake-github-actions (Thomas Weber)
- 8401feb: Test snakemake-github-actions (Thomas Weber)
- 9fa986d: Test snakemake-github-actions (Thomas Weber)
- 0f830f7: Test snakemake-github-actions (Thomas Weber)
- bb82ef6: Test snakemake-github-actions (Thomas Weber)
- 7f9cb2f: Test snakemake-github-actions (Thomas Weber)
- 333f00d: Test snakemake-github-actions (Thomas Weber)
- 5125911: Test snakemake-github-actions (Thomas Weber)
- afe6a6b: Test snakemake-github-actions (Thomas Weber)
- cc4c4fa: Test snakemake-github-actions (Thomas Weber)
- 5a0dfcd: Test snakemake-github-actions (Thomas Weber)
- 3c5ef05: Test snakemake-github-actions (Thomas Weber)
- b557410: Test snakemake-github-actions (Thomas Weber)
- aedf6d5: Test snakemake-github-actions (Thomas Weber)
- ea0059e: Test snakemake-github-actions (Thomas Weber)
- 2e293a7: Test github actions to create docker image (Thomas Weber)
- 5cc66f5: Test github actions to create docker image (Thomas Weber)
- bd33a62: Test github actions to create docker image (Thomas Weber)
- d0cae55: Test github actions to create docker image (Thomas Weber)
- 9a9d0c1: Test github actions to create docker image (Thomas Weber)
- 9e34885: Test github actions to create docker image (Thomas Weber)
- df8d618: Test github actions to create docker image (Thomas Weber)
- 5fa...
1.5.1
mosaicatcher-pipeline 1.3
mosaicatcher-pipeline 1.0
Add files via upload