From a7cb893e65feae8e2ec2ef87a2eb72ad868bd049 Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Mon, 30 Sep 2024 12:42:16 +0000 Subject: [PATCH 1/4] chore(master): release MPRAsnakeflow 0.2.0 --- .release-please-manifest.json | 2 +- CHANGELOG.md | 55 +++++++++++++++++++++++++++++++++++ version.txt | 2 +- 3 files changed, 57 insertions(+), 2 deletions(-) diff --git a/.release-please-manifest.json b/.release-please-manifest.json index 466df71..2be9c43 100644 --- a/.release-please-manifest.json +++ b/.release-please-manifest.json @@ -1,3 +1,3 @@ { - ".": "0.1.0" + ".": "0.2.0" } diff --git a/CHANGELOG.md b/CHANGELOG.md index be3e20d..c9d1643 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,60 @@ # Changelog +## [0.2.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.1.0...MPRAsnakeflow-v0.2.0) (2024-09-30) + + +### ⚠ BREAKING CHANGES + +* pseudocounts where not used correctly when RNA or DNA set to 0 +* DNA and RNA join correction +* pseudocounts where not used correctly when RNA or DNA set to 0 + +### Features + +* Add assignment_merge thread configuration ([26e68c2](https://github.com/kircherlab/MPRAsnakeflow/commit/26e68c26f315c524cf28692d636127fbf3bdeb2b)) +* add formatters ([e589376](https://github.com/kircherlab/MPRAsnakeflow/commit/e589376d48cdcbbce30eee6a3009837b8853b4c4)) +* better assignment BC statistics ([00187e6](https://github.com/kircherlab/MPRAsnakeflow/commit/00187e689b2fad10fd317aa2efbd0214fad14434)) +* configurable min mapping quality ([28045ae](https://github.com/kircherlab/MPRAsnakeflow/commit/28045aea23d6fa03f3883b3dc44b3cbc3e8f6205)) +* extending figure width ([8bf81c4](https://github.com/kircherlab/MPRAsnakeflow/commit/8bf81c45e45f9b4c23856c0915bd527f9699b6cd)) +* faster design check ([315b402](https://github.com/kircherlab/MPRAsnakeflow/commit/315b402499d92850382d4110e153602020381e8a)) +* fastq-join implementation ([aaf5315](https://github.com/kircherlab/MPRAsnakeflow/commit/aaf5315364ebb3e3117c3996c2fc357aa9c4d595)) +* fewer print mesaaages in BCCounts ([a1dc242](https://github.com/kircherlab/MPRAsnakeflow/commit/a1dc2421008ee2b5d223724cdb5d9b6181b26fb3)) +* make filtering consistent ([5f7a4c5](https://github.com/kircherlab/MPRAsnakeflow/commit/5f7a4c5a2a3389a75b8d6b7e9aaf34485127b3a4)) +* master variant table ([6bda47c](https://github.com/kircherlab/MPRAsnakeflow/commit/6bda47c78021bc1728bb81a716f5e6daaf6ac084)) +* new final output file with merged replicates ([66cf017](https://github.com/kircherlab/MPRAsnakeflow/commit/66cf0172cb6b556e507be4daabf7e859447787f3)) +* only link assignment fasta when possible ([d7d3822](https://github.com/kircherlab/MPRAsnakeflow/commit/d7d3822933c98d790f3c96bcbfdef1a7ea70c7df)), closes [#50](https://github.com/kircherlab/MPRAsnakeflow/issues/50) +* remove space, speedup BC extraction ([70e9bd0](https://github.com/kircherlab/MPRAsnakeflow/commit/70e9bd06b91ccb37333e0a69c47917a5eacbf639)) +* replace merging by NGmerge ([0aa8cad](https://github.com/kircherlab/MPRAsnakeflow/commit/0aa8cad6884a953f9c89a2fdd7af397e4e9ccf3e)) +* snakemake 8 compatibility ([cf38ed9](https://github.com/kircherlab/MPRAsnakeflow/commit/cf38ed9de68367d0d1700ccff262e91ad6f1fbc0)) +* snakemake 8 ready with workflow profile ([d637e1f](https://github.com/kircherlab/MPRAsnakeflow/commit/d637e1fdbebfca0616d944101898fbf522df9c82)) +* statistic for assignment workflow ([10c3b26](https://github.com/kircherlab/MPRAsnakeflow/commit/10c3b2677ada59925ddd3de777f7488c9a20e981)) +* using reverese compelment BCs ([d009a6c](https://github.com/kircherlab/MPRAsnakeflow/commit/d009a6c3de7de50a210479b73f5d41969287e234)) + + +### Bug Fixes + +* batch size issue in sort ([487ba8c](https://github.com/kircherlab/MPRAsnakeflow/commit/487ba8ce059517030fcab3708c3cea40ac210f7e)) +* correct use of assignment configs ([58b64f1](https://github.com/kircherlab/MPRAsnakeflow/commit/58b64f1e753477f7410233ac546701ddbd60f9f2)) +* corrected qc_report_assoc ([afb0127](https://github.com/kircherlab/MPRAsnakeflow/commit/afb012750bc1c3c39f2348b283c23ff97695f672)) +* Detach from anaconda ([#122](https://github.com/kircherlab/MPRAsnakeflow/issues/122)) ([16bcea2](https://github.com/kircherlab/MPRAsnakeflow/commit/16bcea2f04190a5965ad1865cf30f6dd44f1b6a0)) +* DNA and RNA join correction ([7214743](https://github.com/kircherlab/MPRAsnakeflow/commit/7214743008dc6796077e45e62646174ffaf52290)) +* filter config ([38ee37e](https://github.com/kircherlab/MPRAsnakeflow/commit/38ee37ecfcf4a71b840575504811512e0d64609a)) +* issue with stats and asisgnment ([d935fa1](https://github.com/kircherlab/MPRAsnakeflow/commit/d935fa1f62825dfdcd2cd77e4c73bc37686519a0)) +* memory resources for bbmap ([#123](https://github.com/kircherlab/MPRAsnakeflow/issues/123)) ([af93f58](https://github.com/kircherlab/MPRAsnakeflow/commit/af93f588e9387ddf91197f5587d36c3481499b38)) +* missing final_counts_umi_samplerer in cluster conf ([283c271](https://github.com/kircherlab/MPRAsnakeflow/commit/283c271629e99aee2558a63c1c1e424c02c42816)) +* plots per insert only used last experiment. not all. ([c2fd82b](https://github.com/kircherlab/MPRAsnakeflow/commit/c2fd82b6d4b545cc3a1acc5ecb145eb3c93af49d)) +* pseudocounts where not used correctly when RNA or DNA set to 0 ([d2483f9](https://github.com/kircherlab/MPRAsnakeflow/commit/d2483f9c7724e0b63cec4f251519d449831ecf04)) +* pseudocounts where not used correctly when RNA or DNA set to 0 ([2ab3c62](https://github.com/kircherlab/MPRAsnakeflow/commit/2ab3c6260388b32c0d91527f98c02668049d17e8)) +* remove illegal characters from reference ([0ebee81](https://github.com/kircherlab/MPRAsnakeflow/commit/0ebee81d74f3f6170ce4b8083e18c746550154db)) +* rename barcoe output header ([635f043](https://github.com/kircherlab/MPRAsnakeflow/commit/635f0431c78d3d5bf9b77a16f6ce26d9ff6c82c2)) +* rule make_master_tables fix ([df42845](https://github.com/kircherlab/MPRAsnakeflow/commit/df42845b6dfa9a7b64f187b38f1f15518f3e4a31)) +* SCRIPTS_DIR changed from common.smk ([f459f83](https://github.com/kircherlab/MPRAsnakeflow/commit/f459f83423921f3183a20bda2233d6d1691c9321)) +* statistic total counts ([6381b92](https://github.com/kircherlab/MPRAsnakeflow/commit/6381b928fd6c14eb16801a459b8546fa37004c74)) +* typo in report ([ace8cca](https://github.com/kircherlab/MPRAsnakeflow/commit/ace8ccacb3d7ece04af43c9b0b1dc9c9c087a2c4)) +* upgrade code to new pandas version ([aaea236](https://github.com/kircherlab/MPRAsnakeflow/commit/aaea236bc83f459e7a6c2d3fee96d49c79762325)) +* using correct threads ([6dcad7d](https://github.com/kircherlab/MPRAsnakeflow/commit/6dcad7d34173f37d4538644b1ba0d918afd8f149)) +* using multiple fastq inputs in counts ([95935cf](https://github.com/kircherlab/MPRAsnakeflow/commit/95935cfe69956ca50307a9c6a774c4b96dff860f)) + ## [0.1.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.0.1...MPRAsnakeflow-v0.1.0) (2024-09-18) First release of MPRAsnakeflow! diff --git a/version.txt b/version.txt index 6e8bf73..0ea3a94 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -0.1.0 +0.2.0 From d23266ba4e615e6420c0f2c83b2b3e9dc3634af5 Mon Sep 17 00:00:00 2001 From: Max Date: Mon, 30 Sep 2024 14:46:08 +0200 Subject: [PATCH 2/4] Update .release-please-manifest.json --- .release-please-manifest.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.release-please-manifest.json b/.release-please-manifest.json index 2be9c43..a915e8c 100644 --- a/.release-please-manifest.json +++ b/.release-please-manifest.json @@ -1,3 +1,3 @@ { - ".": "0.2.0" + ".": "0.1.1" } From 0529b5863b5551c8b16b02a268bc5fbeea7a2957 Mon Sep 17 00:00:00 2001 From: Max Date: Mon, 30 Sep 2024 14:46:28 +0200 Subject: [PATCH 3/4] Update version.txt --- version.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/version.txt b/version.txt index 0ea3a94..17e51c3 100644 --- a/version.txt +++ b/version.txt @@ -1 +1 @@ -0.2.0 +0.1.1 From 1e20e6ebc5f5e04d59f75f08207183644a53cdc6 Mon Sep 17 00:00:00 2001 From: Max Date: Mon, 30 Sep 2024 14:48:23 +0200 Subject: [PATCH 4/4] Update CHANGELOG.md --- CHANGELOG.md | 50 +------------------------------------------------- 1 file changed, 1 insertion(+), 49 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c9d1643..9f1a35e 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,59 +1,11 @@ # Changelog -## [0.2.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.1.0...MPRAsnakeflow-v0.2.0) (2024-09-30) - - -### ⚠ BREAKING CHANGES - -* pseudocounts where not used correctly when RNA or DNA set to 0 -* DNA and RNA join correction -* pseudocounts where not used correctly when RNA or DNA set to 0 - -### Features - -* Add assignment_merge thread configuration ([26e68c2](https://github.com/kircherlab/MPRAsnakeflow/commit/26e68c26f315c524cf28692d636127fbf3bdeb2b)) -* add formatters ([e589376](https://github.com/kircherlab/MPRAsnakeflow/commit/e589376d48cdcbbce30eee6a3009837b8853b4c4)) -* better assignment BC statistics ([00187e6](https://github.com/kircherlab/MPRAsnakeflow/commit/00187e689b2fad10fd317aa2efbd0214fad14434)) -* configurable min mapping quality ([28045ae](https://github.com/kircherlab/MPRAsnakeflow/commit/28045aea23d6fa03f3883b3dc44b3cbc3e8f6205)) -* extending figure width ([8bf81c4](https://github.com/kircherlab/MPRAsnakeflow/commit/8bf81c45e45f9b4c23856c0915bd527f9699b6cd)) -* faster design check ([315b402](https://github.com/kircherlab/MPRAsnakeflow/commit/315b402499d92850382d4110e153602020381e8a)) -* fastq-join implementation ([aaf5315](https://github.com/kircherlab/MPRAsnakeflow/commit/aaf5315364ebb3e3117c3996c2fc357aa9c4d595)) -* fewer print mesaaages in BCCounts ([a1dc242](https://github.com/kircherlab/MPRAsnakeflow/commit/a1dc2421008ee2b5d223724cdb5d9b6181b26fb3)) -* make filtering consistent ([5f7a4c5](https://github.com/kircherlab/MPRAsnakeflow/commit/5f7a4c5a2a3389a75b8d6b7e9aaf34485127b3a4)) -* master variant table ([6bda47c](https://github.com/kircherlab/MPRAsnakeflow/commit/6bda47c78021bc1728bb81a716f5e6daaf6ac084)) -* new final output file with merged replicates ([66cf017](https://github.com/kircherlab/MPRAsnakeflow/commit/66cf0172cb6b556e507be4daabf7e859447787f3)) -* only link assignment fasta when possible ([d7d3822](https://github.com/kircherlab/MPRAsnakeflow/commit/d7d3822933c98d790f3c96bcbfdef1a7ea70c7df)), closes [#50](https://github.com/kircherlab/MPRAsnakeflow/issues/50) -* remove space, speedup BC extraction ([70e9bd0](https://github.com/kircherlab/MPRAsnakeflow/commit/70e9bd06b91ccb37333e0a69c47917a5eacbf639)) -* replace merging by NGmerge ([0aa8cad](https://github.com/kircherlab/MPRAsnakeflow/commit/0aa8cad6884a953f9c89a2fdd7af397e4e9ccf3e)) -* snakemake 8 compatibility ([cf38ed9](https://github.com/kircherlab/MPRAsnakeflow/commit/cf38ed9de68367d0d1700ccff262e91ad6f1fbc0)) -* snakemake 8 ready with workflow profile ([d637e1f](https://github.com/kircherlab/MPRAsnakeflow/commit/d637e1fdbebfca0616d944101898fbf522df9c82)) -* statistic for assignment workflow ([10c3b26](https://github.com/kircherlab/MPRAsnakeflow/commit/10c3b2677ada59925ddd3de777f7488c9a20e981)) -* using reverese compelment BCs ([d009a6c](https://github.com/kircherlab/MPRAsnakeflow/commit/d009a6c3de7de50a210479b73f5d41969287e234)) - +## [0.1.1](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.1.0...MPRAsnakeflow-v0.1.1) (2024-09-30) ### Bug Fixes -* batch size issue in sort ([487ba8c](https://github.com/kircherlab/MPRAsnakeflow/commit/487ba8ce059517030fcab3708c3cea40ac210f7e)) -* correct use of assignment configs ([58b64f1](https://github.com/kircherlab/MPRAsnakeflow/commit/58b64f1e753477f7410233ac546701ddbd60f9f2)) -* corrected qc_report_assoc ([afb0127](https://github.com/kircherlab/MPRAsnakeflow/commit/afb012750bc1c3c39f2348b283c23ff97695f672)) * Detach from anaconda ([#122](https://github.com/kircherlab/MPRAsnakeflow/issues/122)) ([16bcea2](https://github.com/kircherlab/MPRAsnakeflow/commit/16bcea2f04190a5965ad1865cf30f6dd44f1b6a0)) -* DNA and RNA join correction ([7214743](https://github.com/kircherlab/MPRAsnakeflow/commit/7214743008dc6796077e45e62646174ffaf52290)) -* filter config ([38ee37e](https://github.com/kircherlab/MPRAsnakeflow/commit/38ee37ecfcf4a71b840575504811512e0d64609a)) -* issue with stats and asisgnment ([d935fa1](https://github.com/kircherlab/MPRAsnakeflow/commit/d935fa1f62825dfdcd2cd77e4c73bc37686519a0)) * memory resources for bbmap ([#123](https://github.com/kircherlab/MPRAsnakeflow/issues/123)) ([af93f58](https://github.com/kircherlab/MPRAsnakeflow/commit/af93f588e9387ddf91197f5587d36c3481499b38)) -* missing final_counts_umi_samplerer in cluster conf ([283c271](https://github.com/kircherlab/MPRAsnakeflow/commit/283c271629e99aee2558a63c1c1e424c02c42816)) -* plots per insert only used last experiment. not all. ([c2fd82b](https://github.com/kircherlab/MPRAsnakeflow/commit/c2fd82b6d4b545cc3a1acc5ecb145eb3c93af49d)) -* pseudocounts where not used correctly when RNA or DNA set to 0 ([d2483f9](https://github.com/kircherlab/MPRAsnakeflow/commit/d2483f9c7724e0b63cec4f251519d449831ecf04)) -* pseudocounts where not used correctly when RNA or DNA set to 0 ([2ab3c62](https://github.com/kircherlab/MPRAsnakeflow/commit/2ab3c6260388b32c0d91527f98c02668049d17e8)) -* remove illegal characters from reference ([0ebee81](https://github.com/kircherlab/MPRAsnakeflow/commit/0ebee81d74f3f6170ce4b8083e18c746550154db)) -* rename barcoe output header ([635f043](https://github.com/kircherlab/MPRAsnakeflow/commit/635f0431c78d3d5bf9b77a16f6ce26d9ff6c82c2)) -* rule make_master_tables fix ([df42845](https://github.com/kircherlab/MPRAsnakeflow/commit/df42845b6dfa9a7b64f187b38f1f15518f3e4a31)) -* SCRIPTS_DIR changed from common.smk ([f459f83](https://github.com/kircherlab/MPRAsnakeflow/commit/f459f83423921f3183a20bda2233d6d1691c9321)) -* statistic total counts ([6381b92](https://github.com/kircherlab/MPRAsnakeflow/commit/6381b928fd6c14eb16801a459b8546fa37004c74)) -* typo in report ([ace8cca](https://github.com/kircherlab/MPRAsnakeflow/commit/ace8ccacb3d7ece04af43c9b0b1dc9c9c087a2c4)) -* upgrade code to new pandas version ([aaea236](https://github.com/kircherlab/MPRAsnakeflow/commit/aaea236bc83f459e7a6c2d3fee96d49c79762325)) -* using correct threads ([6dcad7d](https://github.com/kircherlab/MPRAsnakeflow/commit/6dcad7d34173f37d4538644b1ba0d918afd8f149)) -* using multiple fastq inputs in counts ([95935cf](https://github.com/kircherlab/MPRAsnakeflow/commit/95935cfe69956ca50307a9c6a774c4b96dff860f)) ## [0.1.0](https://github.com/kircherlab/MPRAsnakeflow/compare/MPRAsnakeflow-v0.0.1...MPRAsnakeflow-v0.1.0) (2024-09-18)