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socialgene · Feb 22, 2024 · 464163e · 464163e
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diff --git a/.github/CONTRIBUTING.html b/.github/CONTRIBUTING.html
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
@@ -50,7 +50,6 @@ These tests are run both with the latest available version of `Nextflow` and als
 - Fix the bug, and bump version (X.Y.Z+1).
 - A PR should be made on `master` from patch to directly this particular bug.
 
-
 ## Pipeline contribution conventions
 
 To make SocialGene's Nextflow code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written.

diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1 +0,0 @@
-

diff --git a/.github/workflows/docker.yml b/.github/workflows/docker.yml
@@ -14,10 +14,7 @@ jobs:
     #      contents: read
     strategy:
       matrix:
-        env:
-          [
-            ["sgpy-base", "dockerfiles/sgpy/sgpy_base"],
-          ]
+        env: [["sgpy-base", "dockerfiles/sgpy/sgpy_base"]]
     steps:
       - name: Checkout
         uses: actions/checkout@v3

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,241 +2,208 @@
 
 ## [0.4.2](https://github.com/socialgene/sgnf/compare/v0.4.1...v0.4.2) (2023-12-08)
 
-
 ### Bug Fixes
 
-* fixes [#89](https://github.com/socialgene/sgnf/issues/89) ([0f1ce5c](https://github.com/socialgene/sgnf/commit/0f1ce5cb20ddbb5868e8b534aa4de6d9400a69f9))
+- fixes [#89](https://github.com/socialgene/sgnf/issues/89) ([0f1ce5c](https://github.com/socialgene/sgnf/commit/0f1ce5cb20ddbb5868e8b534aa4de6d9400a69f9))
 
 ## [0.4.1](https://github.com/socialgene/sgnf/compare/v0.4.0...v0.4.1) (2023-11-18)
 
-
 ### Bug Fixes
 
-* change from tar to gz ([7dde2fd](https://github.com/socialgene/sgnf/commit/7dde2fdb72e1d5114ed8a0ddf981357205e0c75d))
+- change from tar to gz ([7dde2fd](https://github.com/socialgene/sgnf/commit/7dde2fdb72e1d5114ed8a0ddf981357205e0c75d))
 
 ## [0.4.0](https://github.com/socialgene/sgnf/compare/v0.3.12...v0.4.0) (2023-11-18)
 
-
 ### Features
 
-* antismash 7 ([8178835](https://github.com/socialgene/sgnf/commit/8178835f9033d67100f20dc8073a3a056d6c6f18))
-
+- antismash 7 ([8178835](https://github.com/socialgene/sgnf/commit/8178835f9033d67100f20dc8073a3a056d6c6f18))
 
 ### Bug Fixes
 
-* deprecate 6.1 antismash ([bda70d0](https://github.com/socialgene/sgnf/commit/bda70d0c7a319dead3d30f7adee83961268955bc))
+- deprecate 6.1 antismash ([bda70d0](https://github.com/socialgene/sgnf/commit/bda70d0c7a319dead3d30f7adee83961268955bc))
 
 ## [0.3.12](https://github.com/socialgene/sgnf/compare/v0.3.11...v0.3.12) (2023-11-17)
 
-
 ### Bug Fixes
 
-* hmmparse ([4c771b9](https://github.com/socialgene/sgnf/commit/4c771b9d073b3cab699201bb9f4df6e284b55d18))
+- hmmparse ([4c771b9](https://github.com/socialgene/sgnf/commit/4c771b9d073b3cab699201bb9f4df6e284b55d18))
 
 ## [0.3.11](https://github.com/socialgene/sgnf/compare/v0.3.10...v0.3.11) (2023-11-17)
 
-
 ### Bug Fixes
 
-* update hmmsearch parsing ([7cc82b0](https://github.com/socialgene/sgnf/commit/7cc82b007270dba5f12887a237f0a3f3bd7eccd5))
+- update hmmsearch parsing ([7cc82b0](https://github.com/socialgene/sgnf/commit/7cc82b007270dba5f12887a237f0a3f3bd7eccd5))
 
 ## [0.3.10](https://github.com/socialgene/sgnf/compare/v0.3.9...v0.3.10) (2023-11-17)
 
-
 ### Miscellaneous Chores
 
-* release 0.3.10 ([2a06777](https://github.com/socialgene/sgnf/commit/2a0677723337b0a2b09d44dd1d7e101a408a3f45))
+- release 0.3.10 ([2a06777](https://github.com/socialgene/sgnf/commit/2a0677723337b0a2b09d44dd1d7e101a408a3f45))
 
 ## [0.3.9](https://github.com/socialgene/sgnf/compare/v0.3.8...v0.3.9) (2023-11-17)
 
-
 ### Bug Fixes
 
-* . ([227eed0](https://github.com/socialgene/sgnf/commit/227eed0bca1a7192c3f63b64d68f260e8c0071bc))
-* add control for HMMSEARCH_IEVALUE in hmmsearch parse ([0b5cf04](https://github.com/socialgene/sgnf/commit/0b5cf0432a9b6bd2aea43a56c23f51bd1dfa5320))
-* add job length to hcondor stdout ([a3741db](https://github.com/socialgene/sgnf/commit/a3741dbb16ece9c20594f32a63f16b31bb0d95d1))
-* add std cov for mmseqs ([9745704](https://github.com/socialgene/sgnf/commit/974570492907cb2f816f2a83356bb68d344e6549))
-* switch ncbi ftp to https ([7c3eb17](https://github.com/socialgene/sgnf/commit/7c3eb175b8a41d985365e0bd6bc6cb634a280a21))
+- . ([227eed0](https://github.com/socialgene/sgnf/commit/227eed0bca1a7192c3f63b64d68f260e8c0071bc))
+- add control for HMMSEARCH_IEVALUE in hmmsearch parse ([0b5cf04](https://github.com/socialgene/sgnf/commit/0b5cf0432a9b6bd2aea43a56c23f51bd1dfa5320))
+- add job length to hcondor stdout ([a3741db](https://github.com/socialgene/sgnf/commit/a3741dbb16ece9c20594f32a63f16b31bb0d95d1))
+- add std cov for mmseqs ([9745704](https://github.com/socialgene/sgnf/commit/974570492907cb2f816f2a83356bb68d344e6549))
+- switch ncbi ftp to https ([7c3eb17](https://github.com/socialgene/sgnf/commit/7c3eb175b8a41d985365e0bd6bc6cb634a280a21))
 
 ## [0.3.8](https://github.com/socialgene/sgnf/compare/v0.3.7...v0.3.8) (2023-11-10)
 
-
 ### Bug Fixes
 
-* add option to not store antismash tar ([63ab839](https://github.com/socialgene/sgnf/commit/63ab839a17db138274e8775ef0033918cefec4f4))
+- add option to not store antismash tar ([63ab839](https://github.com/socialgene/sgnf/commit/63ab839a17db138274e8775ef0033918cefec4f4))
 
 ## [0.3.7](https://github.com/socialgene/sgnf/compare/v0.3.6...v0.3.7) (2023-11-10)
 
-
 ### Bug Fixes
 
-* slurm overwrite in custom configs ([f13c77f](https://github.com/socialgene/sgnf/commit/f13c77f3971a708903342fbc2c29813cd4ed004a))
+- slurm overwrite in custom configs ([f13c77f](https://github.com/socialgene/sgnf/commit/f13c77f3971a708903342fbc2c29813cd4ed004a))
 
 ## [0.3.6](https://github.com/socialgene/sgnf/compare/v0.3.5...v0.3.6) (2023-11-10)
 
-
 ### Miscellaneous Chores
 
-* release 0.3.6 ([b569cea](https://github.com/socialgene/sgnf/commit/b569cea155792807053d35a1d665a9e375aa60cc))
+- release 0.3.6 ([b569cea](https://github.com/socialgene/sgnf/commit/b569cea155792807053d35a1d665a9e375aa60cc))
 
 ## [0.3.5](https://github.com/socialgene/sgnf/compare/v0.3.4...v0.3.5) (2023-11-10)
 
-
 ### Bug Fixes
 
-* add antismash version to reports ([fc59e1c](https://github.com/socialgene/sgnf/commit/fc59e1c658f0e8426de06ca37308ad6ecf5e3239))
-* ncbi datasets ([138c9b8](https://github.com/socialgene/sgnf/commit/138c9b8fa0c2dd3c0a0b5de01a773fd4d3bfd630))
+- add antismash version to reports ([fc59e1c](https://github.com/socialgene/sgnf/commit/fc59e1c658f0e8426de06ca37308ad6ecf5e3239))
+- ncbi datasets ([138c9b8](https://github.com/socialgene/sgnf/commit/138c9b8fa0c2dd3c0a0b5de01a773fd4d3bfd630))
 
 ## [0.3.4](https://github.com/socialgene/sgnf/compare/v0.3.3...v0.3.4) (2023-11-10)
 
-
 ### Bug Fixes
 
-* move antismash cpus and mem to config ([1a74e81](https://github.com/socialgene/sgnf/commit/1a74e81ed09da0dd72bdc7803c9b4fe05082bbe7))
-* prevent antismash from erroring on seqs w/o proteins ([f7065d0](https://github.com/socialgene/sgnf/commit/f7065d0361cda8496e51e7aa5f023e2a810c2e76))
-* remove and comment out currently unused computation ([7677748](https://github.com/socialgene/sgnf/commit/7677748e0c30b883abae20d7c1c18c79ca290c4c))
-* update strep config ([ddd2299](https://github.com/socialgene/sgnf/commit/ddd2299357ddaaaae20145dee861f4f5fb34f901))
+- move antismash cpus and mem to config ([1a74e81](https://github.com/socialgene/sgnf/commit/1a74e81ed09da0dd72bdc7803c9b4fe05082bbe7))
+- prevent antismash from erroring on seqs w/o proteins ([f7065d0](https://github.com/socialgene/sgnf/commit/f7065d0361cda8496e51e7aa5f023e2a810c2e76))
+- remove and comment out currently unused computation ([7677748](https://github.com/socialgene/sgnf/commit/7677748e0c30b883abae20d7c1c18c79ca290c4c))
+- update strep config ([ddd2299](https://github.com/socialgene/sgnf/commit/ddd2299357ddaaaae20145dee861f4f5fb34f901))
 
 ## [0.3.3](https://github.com/socialgene/sgnf/compare/v0.3.2...v0.3.3) (2023-11-09)
 
-
 ### Bug Fixes
 
-* neo4j docker Java must be pinned to jdk 17 ([25c0f32](https://github.com/socialgene/sgnf/commit/25c0f32c87eed59373ee3af582b57cb07ac2e8a0))
-* rm datasets file input, and fix version output since it changed in v15 ([d2c4d90](https://github.com/socialgene/sgnf/commit/d2c4d9070d45d2841099ee86715cb9d013d80726))
+- neo4j docker Java must be pinned to jdk 17 ([25c0f32](https://github.com/socialgene/sgnf/commit/25c0f32c87eed59373ee3af582b57cb07ac2e8a0))
+- rm datasets file input, and fix version output since it changed in v15 ([d2c4d90](https://github.com/socialgene/sgnf/commit/d2c4d9070d45d2841099ee86715cb9d013d80726))
 
 ## [0.3.2](https://github.com/socialgene/sgnf/compare/v0.3.1...v0.3.2) (2023-11-08)
 
-
 ### Bug Fixes
 
-* release-please ([682a161](https://github.com/socialgene/sgnf/commit/682a1612dbc4d6cfed6d3de082eb0db0f5e389c8))
-
+- release-please ([682a161](https://github.com/socialgene/sgnf/commit/682a1612dbc4d6cfed6d3de082eb0db0f5e389c8))
 
 ### Miscellaneous Chores
 
-* release 0.3.2 ([53f839f](https://github.com/socialgene/sgnf/commit/53f839faee7eb53ed786f9809df2250015d4c32b))
+- release 0.3.2 ([53f839f](https://github.com/socialgene/sgnf/commit/53f839faee7eb53ed786f9809df2250015d4c32b))
 
 ## [0.3.1](https://github.com/socialgene/sgnf/compare/v0.3.0...v0.3.1) (2023-11-08)
 
-
 ### Bug Fixes
 
-* docker sgpy-base ([#71](https://github.com/socialgene/sgnf/issues/71)) ([ea26118](https://github.com/socialgene/sgnf/commit/ea261186da643048d02b2b2a47a05f336eebedf9))
+- docker sgpy-base ([#71](https://github.com/socialgene/sgnf/issues/71)) ([ea26118](https://github.com/socialgene/sgnf/commit/ea261186da643048d02b2b2a47a05f336eebedf9))
 
 ## [0.3.0](https://github.com/socialgene/sgnf/compare/v0.2.6...v0.3.0) (2023-11-08)
 
-
 ### Features
 
-* new release ([#69](https://github.com/socialgene/sgnf/issues/69)) ([2ae0668](https://github.com/socialgene/sgnf/commit/2ae0668921ac0987b54ae5bd5c710d9f2df6ca5c))
+- new release ([#69](https://github.com/socialgene/sgnf/issues/69)) ([2ae0668](https://github.com/socialgene/sgnf/commit/2ae0668921ac0987b54ae5bd5c710d9f2df6ca5c))
 
 ## [0.2.6](https://github.com/socialgene/sgnf/compare/v0.2.5...v0.2.6) (2023-10-14)
 
-
 ### Bug Fixes
 
-* update ncbi dataset cli ([e3af2b8](https://github.com/socialgene/sgnf/commit/e3af2b876eabfd8d27ded5ea6fe8abf90097bba2))
+- update ncbi dataset cli ([e3af2b8](https://github.com/socialgene/sgnf/commit/e3af2b876eabfd8d27ded5ea6fe8abf90097bba2))
 
 ## [0.2.5](https://github.com/socialgene/sgnf/compare/v0.2.4...v0.2.5) (2023-08-30)
 
-
 ### Bug Fixes
 
-* args in mmseqs and change to comma-delimited ([5963bc7](https://github.com/socialgene/sgnf/commit/5963bc78cee22d9cdedf83fd0f3dfffd1375de79))
-* mac compatibility ([e968c7b](https://github.com/socialgene/sgnf/commit/e968c7b3759471b90ec988867e4b78fce4be33b1))
-* output an empty conf directory ([dce91cc](https://github.com/socialgene/sgnf/commit/dce91cc55cbb0e4619905ed3907e26247bb55cd2))
+- args in mmseqs and change to comma-delimited ([5963bc7](https://github.com/socialgene/sgnf/commit/5963bc78cee22d9cdedf83fd0f3dfffd1375de79))
+- mac compatibility ([e968c7b](https://github.com/socialgene/sgnf/commit/e968c7b3759471b90ec988867e4b78fce4be33b1))
+- output an empty conf directory ([dce91cc](https://github.com/socialgene/sgnf/commit/dce91cc55cbb0e4619905ed3907e26247bb55cd2))
 
 ## [0.2.4](https://github.com/socialgene/sgnf/compare/v0.2.3...v0.2.4) (2023-07-03)
 
-
 ### Bug Fixes
 
-* fix configs for nf-tower use ([364a40d](https://github.com/socialgene/sgnf/commit/364a40d485b34da5262232916a32786bf96dd3e1))
+- fix configs for nf-tower use ([364a40d](https://github.com/socialgene/sgnf/commit/364a40d485b34da5262232916a32786bf96dd3e1))
 
 ## [0.2.3](https://github.com/socialgene/sgnf/compare/v0.2.2...v0.2.3) (2023-07-03)
 
-
 ### Bug Fixes
 
-* null hmmlist ([e65d199](https://github.com/socialgene/sgnf/commit/e65d1997da40a4d6a9c395373c07aeffcc4bf11e))
+- null hmmlist ([e65d199](https://github.com/socialgene/sgnf/commit/e65d1997da40a4d6a9c395373c07aeffcc4bf11e))
 
 ## [0.2.2](https://github.com/socialgene/sgnf/compare/v0.2.1...v0.2.2) (2023-07-03)
 
-
 ### Bug Fixes
 
-* remove unused protein_info_table ([be4cb0d](https://github.com/socialgene/sgnf/commit/be4cb0d78d870c3628fbf74f840d2ca5a2f23c90))
+- remove unused protein_info_table ([be4cb0d](https://github.com/socialgene/sgnf/commit/be4cb0d78d870c3628fbf74f840d2ca5a2f23c90))
 
 ## [0.2.1](https://github.com/socialgene/sgnf/compare/v0.2.0...v0.2.1) (2023-07-03)
 
-
 ### Bug Fixes
 
-* bump sgpy version ([186c4b1](https://github.com/socialgene/sgnf/commit/186c4b11371762d6412f29589e336899ef4d0bb2))
+- bump sgpy version ([186c4b1](https://github.com/socialgene/sgnf/commit/186c4b11371762d6412f29589e336899ef4d0bb2))
 
 ## [0.2.0](https://github.com/socialgene/sgnf/compare/v0.1.7...v0.2.0) (2023-07-03)
 
-
 ### Features
 
-* ([#57](https://github.com/socialgene/sgnf/issues/57)) ([5fba835](https://github.com/socialgene/sgnf/commit/5fba835979d153b8b8bcf669783f876c30081856))
+- ([#57](https://github.com/socialgene/sgnf/issues/57)) ([5fba835](https://github.com/socialgene/sgnf/commit/5fba835979d153b8b8bcf669783f876c30081856))
 
 ## [0.1.7](https://github.com/socialgene/sgnf/compare/v0.1.6...v0.1.7) (2023-07-03)
 
-
 ### Bug Fixes
 
-* bump sgpy ([6e3d05d](https://github.com/socialgene/sgnf/commit/6e3d05d05a0f04531ee3a1a5c33e05aa2d112ccb))
+- bump sgpy ([6e3d05d](https://github.com/socialgene/sgnf/commit/6e3d05d05a0f04531ee3a1a5c33e05aa2d112ccb))
 
 ## [0.1.6](https://github.com/socialgene/sgnf/compare/v0.1.5...v0.1.6) (2023-07-02)
 
-
 ### Bug Fixes
 
-* ([#54](https://github.com/socialgene/sgnf/issues/54)) ([1610368](https://github.com/socialgene/sgnf/commit/1610368414004983d6cdfa1942fb1cf97b2613e9))
+- ([#54](https://github.com/socialgene/sgnf/issues/54)) ([1610368](https://github.com/socialgene/sgnf/commit/1610368414004983d6cdfa1942fb1cf97b2613e9))
 
 ## [0.1.5](https://github.com/socialgene/sgnf/compare/v0.1.4...v0.1.5) (2023-06-22)
 
-
 ### Bug Fixes
 
-* antismash and numeric types ([#49](https://github.com/socialgene/sgnf/issues/49)) ([744d955](https://github.com/socialgene/sgnf/commit/744d9553cedb38a9ca0b695c9f38c112a63453aa))
+- antismash and numeric types ([#49](https://github.com/socialgene/sgnf/issues/49)) ([744d955](https://github.com/socialgene/sgnf/commit/744d9553cedb38a9ca0b695c9f38c112a63453aa))
 
 ## [0.1.4](https://github.com/socialgene/sgnf/compare/v0.1.3...v0.1.4) (2023-06-22)
 
-
 ### Bug Fixes
 
-* antismash ([#47](https://github.com/socialgene/sgnf/issues/47)) ([8a22868](https://github.com/socialgene/sgnf/commit/8a22868360c9ac10994ef7d5649af25e5d829576))
+- antismash ([#47](https://github.com/socialgene/sgnf/issues/47)) ([8a22868](https://github.com/socialgene/sgnf/commit/8a22868360c9ac10994ef7d5649af25e5d829576))
 
 ## [0.1.3](https://github.com/socialgene/sgnf/compare/v0.1.2...v0.1.3) (2023-06-21)
 
-
 ### Bug Fixes
 
-* bump sgpy ([99896f6](https://github.com/socialgene/sgnf/commit/99896f6a8454ab14b117da0155f39df9e93b3856))
+- bump sgpy ([99896f6](https://github.com/socialgene/sgnf/commit/99896f6a8454ab14b117da0155f39df9e93b3856))
 
 ## [0.1.2](https://github.com/socialgene/sgnf/compare/v0.1.1...v0.1.2) (2023-06-21)
 
-
 ### Bug Fixes
 
-* change default cov id ([#44](https://github.com/socialgene/sgnf/issues/44)) ([b344521](https://github.com/socialgene/sgnf/commit/b34452195c4c30994f9f0197232c5d27a3f1d809))
+- change default cov id ([#44](https://github.com/socialgene/sgnf/issues/44)) ([b344521](https://github.com/socialgene/sgnf/commit/b34452195c4c30994f9f0197232c5d27a3f1d809))
 
 ## [0.1.1](https://github.com/socialgene/sgnf/compare/v0.1.0...v0.1.1) (2023-06-21)
 
-
 ### Bug Fixes
 
-* python code for antismash.jsonl ([b97d5a2](https://github.com/socialgene/sgnf/commit/b97d5a27fb2c0f88d9df36a9939597069c3b7d92))
+- python code for antismash.jsonl ([b97d5a2](https://github.com/socialgene/sgnf/commit/b97d5a27fb2c0f88d9df36a9939597069c3b7d92))
 
 ## [0.1.0](https://github.com/socialgene/sgnf/compare/v0.0.6...v0.1.0) (2023-06-21)
 
-
 ### Features
 
-* create antismash.jsonl ([#41](https://github.com/socialgene/sgnf/issues/41)) ([3087f13](https://github.com/socialgene/sgnf/commit/3087f138422414dd132483cb94b66f0f7129f320))
+- create antismash.jsonl ([#41](https://github.com/socialgene/sgnf/issues/41)) ([3087f13](https://github.com/socialgene/sgnf/commit/3087f138422414dd132483cb94b66f0f7129f320))
 
 ## [0.0.6](https://github.com/socialgene/sgnf/compare/v0.0.5...v0.0.6) (2023-06-21)
 

diff --git a/README.md b/README.md
@@ -1,6 +1,7 @@
 > Note: All releases may introduce breaking changes until the release of v1.0.0
 
 [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/socialgene/sgnf)
+
 <!-- [![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -->
  <!-- [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)  -->
 <!-- [![GitHub Actions CI Status](https://github.com/socialgene/sgnf/workflows/nf-core%20CI/badge.svg)](https://github.com/socialgene/sgnf/actions?query=workflow%3A%22nf-core+CI%22)
@@ -73,8 +74,6 @@ Docker image versions are synced via GitHub actions to be identical to the GitHu
 
 This pipeline can be launched directly from [![Launch on Nextflow Tower](https://img.shields.io/badge/Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/socialgene/sgnf) or [![Run an example with Gitpod](https://img.shields.io/badge/Gitpod-908a85?logo=gitpod)](https://gitpod.io/#https://github.com/socialgene/sgnf)
 
-
 # Schema
 
 ![image](https://github.com/socialgene/sgnf/assets/18691127/36bcf534-3996-4b13-ba5d-f746830ada47)
-
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -31,9 +31,6 @@
                 ]
             }
         },
-        "required": [
-            "sample",
-            "fastq_1"
-        ]
+        "required": ["sample", "fastq_1"]
     }
 }
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -111,9 +111,7 @@
                     "hidden": true
                 }
             },
-            "required": [
-                "outdir"
-            ]
+            "required": ["outdir"]
         },
         "socialgene_parameters": {
             "title": "SocialGene Parameters",