Merge pull request #1 from snakemake-workflows/release-please--branches--main

chore(main): release 1.0.0

Author: dlaehnemann

CHANGELOG.md

@@ -1,5 +1,72 @@
 # Changelog
 
+## 1.0.0 (2025-07-11)
+
+
+### Features
+
+* add cellrange count web summary to report ([02efb6b](https://github.com/snakemake-workflows/cellranger-count/commit/02efb6be12de0fda0b564feeea1605712946b899))
+* add cellranger install from CELLRANGER_TARBALL envvar ([46afa34](https://github.com/snakemake-workflows/cellranger-count/commit/46afa34c3f6093a1965401ad8b3b2901d6096ef9))
+* initial workflow version, untested ([6693269](https://github.com/snakemake-workflows/cellranger-count/commit/6693269a8ba73bb3f5bd96eaea1606ff5049c711))
+* working dryrun GitHub Actions test ([6e666a0](https://github.com/snakemake-workflows/cellranger-count/commit/6e666a05aed5dca81003afdb34b2f3b8104a985d))
+
+
+### Bug Fixes
+
+* .test/config/samples.tsv read2 to R2 (copy-pasta leftover) ([04f3e13](https://github.com/snakemake-workflows/cellranger-count/commit/04f3e135a414f0f72595117697aa498cdb732f69))
+* actually write output to log file ([7e431db](https://github.com/snakemake-workflows/cellranger-count/commit/7e431db367a7aa75900232fc052be7c05cc618ba))
+* add empty resources/refdata directory with .gitignore, so that the dryrun doesn't have a missing input exception ([c7e8baa](https://github.com/snakemake-workflows/cellranger-count/commit/c7e8baa254725b46cea9c3496d11a2dd594957f2))
+* cellranger_count output file names ([c95a490](https://github.com/snakemake-workflows/cellranger-count/commit/c95a490d8e654c7c67e67d9e727c61c83dc789b8))
+* conda env name ([94063e4](https://github.com/snakemake-workflows/cellranger-count/commit/94063e4c8b6a1083eec16bb313e78c1b2c64c077))
+* correct outs-path adjustment ([0a5883f](https://github.com/snakemake-workflows/cellranger-count/commit/0a5883f6f82b0c9035a34a65ac23fce7fe463ea9))
+* correctly add NA column with bind_rows, only if column does not exist ([9c888cd](https://github.com/snakemake-workflows/cellranger-count/commit/9c888cd1721c4c70641cc44db4a94f8690623203))
+* correctly invoke input function get_input_files ([04703f8](https://github.com/snakemake-workflows/cellranger-count/commit/04703f83d6595017dcc1f9328a4ddd8e9c5b7460))
+* correctly reference column in sample_sheet ([1f3b9cc](https://github.com/snakemake-workflows/cellranger-count/commit/1f3b9cc08618dab19c6a2d8dad4ef6a050b3cf21))
+* correctly reference wildcard ([b4862c8](https://github.com/snakemake-workflows/cellranger-count/commit/b4862c84432a6fed94a7d11d9c1fc357459ef9e6))
+* create meaningful rule all ([307bb30](https://github.com/snakemake-workflows/cellranger-count/commit/307bb30c6ce1bd1ea20fb54377744b1ba58bbcda))
+* delete snakemake-created output dir, to allow cellranger to create it anew (and stop it from complaining about it not being a pipestance, sigh) ([7dcfa05](https://github.com/snakemake-workflows/cellranger-count/commit/7dcfa05e5e1bb6c5bb9449c3fbe38427b5bdfad0))
+* ensure that conda bin/ directory is created, even for the empty environment ([d627946](https://github.com/snakemake-workflows/cellranger-count/commit/d627946009cdae946f44f15ba5baabac32e520c9))
+* fastqs path parsing now returns full input path ([090b3fe](https://github.com/snakemake-workflows/cellranger-count/commit/090b3fee396041221fc96f9d30055fcbcea18699))
+* fine-tune .gitignore ([6cba839](https://github.com/snakemake-workflows/cellranger-count/commit/6cba839cf3e386d0ae1041e4d8586d779a6c2078))
+* lane_number lookup ([623efd3](https://github.com/snakemake-workflows/cellranger-count/commit/623efd3f7c9f113d724e884dee20b07d54e42a2f))
+* lane_number lookups and require relative input paths (better portability) ([1db14f9](https://github.com/snakemake-workflows/cellranger-count/commit/1db14f94cac8edccaf95e739ee6a2a8866d6f792))
+* load correct smk file ([f4b97b2](https://github.com/snakemake-workflows/cellranger-count/commit/f4b97b25cca8d689ffd94a04ac692a7028547ecd))
+* make params.mem_gb for --localmem cl argument an int instead of a float ([662ca77](https://github.com/snakemake-workflows/cellranger-count/commit/662ca773b0155261e4e3f818d36dd7ee3195e886))
+* move sample filtering to after library_type column creation ([8dabf74](https://github.com/snakemake-workflows/cellranger-count/commit/8dabf7408b0cd463a995352e6403e55920818e32))
+* NA_character_ was missing trailing underscore ([b51eef6](https://github.com/snakemake-workflows/cellranger-count/commit/b51eef6b17301c9bebb83f47d0236beb8033f45b))
+* omit secondary cellranger analyses (clustering et al.) ([0aed413](https://github.com/snakemake-workflows/cellranger-count/commit/0aed413fc83ad6ab2d2244a25b0badfb32ad0de4))
+* parse all sample_sheet columns as `str` ([2bca1ef](https://github.com/snakemake-workflows/cellranger-count/commit/2bca1ef229678276c99f2e61faecd216bb875a79))
+* path string generation in get_all_samples_fastq ([8bf77c5](https://github.com/snakemake-workflows/cellranger-count/commit/8bf77c546405ac94aeee6f1e3db978f2d6051aa9))
+* properly determine lane number in cellranger_count intput ([5df7ca9](https://github.com/snakemake-workflows/cellranger-count/commit/5df7ca90d1d9905f06d5e83a071ca70e0c8f2c60))
+* quick and dirty fix to get rid of NA row ([74c10a1](https://github.com/snakemake-workflows/cellranger-count/commit/74c10a172b1a959acf2a1e44aba8344ee00386e3))
+* reference to samples, change to sample_sheet ([8aadb28](https://github.com/snakemake-workflows/cellranger-count/commit/8aadb287e58422277a8f8102795241b10671bf57))
+* remove .cloupe file that does not get generated with `--nosecondary` flag ([aa9bded](https://github.com/snakemake-workflows/cellranger-count/commit/aa9bded360f7d2e2e6396711d94f95eeb91e00c0))
+* remove leftover from template ([519735d](https://github.com/snakemake-workflows/cellranger-count/commit/519735d65465f00e73440d6dd6d867f6d3039b89))
+* remove leftover from template workflow ([b187dae](https://github.com/snakemake-workflows/cellranger-count/commit/b187dae668b421a4f215e6b8e4f80f40db9983fe))
+* remove multiext because it would be unsupported multi-level ([ac5e5f2](https://github.com/snakemake-workflows/cellranger-count/commit/ac5e5f2f7e9de3de30912931427e2727dd63790d))
+* restrict workflow test to dryrun, as cellranger can only be installed manually ([74d53b8](https://github.com/snakemake-workflows/cellranger-count/commit/74d53b801100f28a21704c9a218d1d5d61b37725))
+* sample_sheet naming ([4a24924](https://github.com/snakemake-workflows/cellranger-count/commit/4a249249021b978c592c0223d1eae070945451eb))
+* samples schema ([54855ba](https://github.com/snakemake-workflows/cellranger-count/commit/54855ba8089cc4646ae9c2be95083c731a4c7e89))
+* snakefmt and fix double double quote ([b00e229](https://github.com/snakemake-workflows/cellranger-count/commit/b00e2290baefb217d971dc366ae8b852064b2c81))
+* snakemake lint conda environments ([437d19d](https://github.com/snakemake-workflows/cellranger-count/commit/437d19d24908b611640a4dee2ffa54a52260cf7f))
+* symbolic link creation in input linking commands ([a118f87](https://github.com/snakemake-workflows/cellranger-count/commit/a118f87c6693b7e27673bbe4850b38d8f24868c7))
+* syntax (extra quotes) ([194a591](https://github.com/snakemake-workflows/cellranger-count/commit/194a591659e2727c4023a2feb86a79222ed322a5))
+* track main cellranger output directory, to allow for full removal upon failure ([90a4764](https://github.com/snakemake-workflows/cellranger-count/commit/90a476473271f37cf89aa15fc3fea89d1bb025b2))
+* try avoiding contacting anaconda defaults by putting in conda-forge channel ([0d50cfe](https://github.com/snakemake-workflows/cellranger-count/commit/0d50cfe469552a8ced113cdb982e8e16cc59afc3))
+* try moving drop_na further up ([2cf833a](https://github.com/snakemake-workflows/cellranger-count/commit/2cf833a8143ce6e943091a1d9f9905c10d789ec4))
+* try to re-trigger after code changes by not using localrule: True ([831ed4f](https://github.com/snakemake-workflows/cellranger-count/commit/831ed4fbd96431ff284ae143ab0ea5cca6109e34))
+* try with one-sample library csv file ([c173385](https://github.com/snakemake-workflows/cellranger-count/commit/c173385383903aaaefad5478816e6a9d7ebc1413))
+* try without conflicting library csv file ([80e5e69](https://github.com/snakemake-workflows/cellranger-count/commit/80e5e6918ba063ceae30d1630f8f301e5a600e60))
+* turn very quick rules into localrules ([299c7ea](https://github.com/snakemake-workflows/cellranger-count/commit/299c7ea320a02915c8912214a40f49b2085f081a))
+* typo ([641c88b](https://github.com/snakemake-workflows/cellranger-count/commit/641c88b4c69b8a38e077f02ad16109fe159e6eb7))
+* typo ([2b5d307](https://github.com/snakemake-workflows/cellranger-count/commit/2b5d3072fe2a181948377ef84bb84b172145d746))
+* typo in --output-dir arg ([37d4272](https://github.com/snakemake-workflows/cellranger-count/commit/37d42720a4b60d38675e011c45eeeeb46fe9c831))
+* update README.md ([22bfbf2](https://github.com/snakemake-workflows/cellranger-count/commit/22bfbf24fc30c5bf5211694d12560bc1a6d20c5e))
+* use correct flag for symbolic link ([f2a6a9c](https://github.com/snakemake-workflows/cellranger-count/commit/f2a6a9ce4c12f8857ad2a231b54a094b57c29c87))
+* wildcard name ([b552012](https://github.com/snakemake-workflows/cellranger-count/commit/b552012c0fa8fe758573a42b7bd9c9b43619d7af))
+* YAML syntax ([8c1f8cb](https://github.com/snakemake-workflows/cellranger-count/commit/8c1f8cbe7961001f86b573bea159914917c3adac))
+* yamllint ([fbd0ba8](https://github.com/snakemake-workflows/cellranger-count/commit/fbd0ba87e05cb0f6b7f295b3f1aac7da862991f6))
+
 ## 1.0.0 (2025-05-07)