Merge pull request #18 from sanger-tol/dp24_modules_update

Updating all modules
sanger-tol · Feb 8, 2024 · 9e0eca6 · 9e0eca6
2 parents fd4f5bd + 0360796
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,7 +3,52 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [[1.0.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.0.0)] - UNSC Infinity - [2023-10-02]
+## [[0.1.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.0.0)] - UNSC Cradle - [2024-02-08]
+
+### Added
+
+- Subworkflows for both minimap2 and bwamem2 mapping.
+- Subworkflow for Pretext accessory file ingestion.
+- Considerations for other longread datatypes
+
+### Paramters
+
+| Old Version | New Versions  |
+| ----------- | ------------- |
+|             | --aligner     |
+|             | --pacbio_type |
+| --pacbio    | --longread    |
+
+### Software Dependencies
+
+Note, since the pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.
+
+| Module                                 | Old Version | New Versions   |
+| -------------------------------------- | ----------- | -------------- |
+| bamtobed_sort ( bedtools + samtools )  | -           | 2.31.0 + 1.17  |
+| bedtools                               | -           | 2.31.0         |
+| cram_filter_align_bwamem2_fixmate_sort | -           |                |
+| ^ ( samtools + bwamem2 ) ^             | -           | 1.16.1 + 2.2.1 |
+| extract_cov_id ( coreutils )           | -           | 9.1            |
+| extract_repeat ( perl )                | -           | 5.26.2         |
+| extract_telo ( coreutils )             | -           | 9.1            |
+| find_telomere_regions ( gcc )          | -           | 7.1.0          |
+| find_telomere_windows ( java-jdk )     | -           | 8.0.112        |
+| gap_length ( coreutils )               | -           | 9.1            |
+| generate_cram_csv ( samtools )         | -           | 1.17           |
+| get_largest_scaff ( coreutils )        | -           | 9.1            |
+| gnu-sort                               | -           | 8.25           |
+| pretextmap + samtools                  | -           | 0.1.9 + 1.17   |
+| seqtk                                  | -           | 1.4            |
+| tabix                                  | -           | 1.11           |
+| ucsc                                   | -           | 377            |
+| windowmasker (blast)                   | -           | 2.14.0         |
+
+### Dependencies
+
+### Deprecated
+
+## [[0.1.0](https://github.com/sanger-tol/curationpretext/releases/tag/0.1.0)] - UNSC Infinity - [2023-10-02]
 
 Initial release of sanger-tol/curationpretext, created with the [sager-tol](https://nf-co.re/) template.
 

diff --git a/modules.json b/modules.json
@@ -7,112 +7,112 @@
                 "nf-core": {
                     "bedtools/bamtobed": {
                         "branch": "master",
-                        "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
+                        "git_sha": "1d1cb7bfef6cf67fbc7faafa6992ad8bdc3045b3",
                         "installed_by": ["modules"]
                     },
                     "bedtools/genomecov": {
                         "branch": "master",
-                        "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"]
                     },
                     "bedtools/intersect": {
                         "branch": "master",
-                        "git_sha": "c1532c77717ad7c64752b26b0fd9b4556bdef272",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"]
                     },
                     "bedtools/makewindows": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
                         "installed_by": ["modules"]
                     },
                     "bedtools/map": {
                         "branch": "master",
-                        "git_sha": "726ee59cd9360a965d96ea9ea8770f16b8ddd6cc",
+                        "git_sha": "3b248b84694d1939ac4bb33df84bf6233a34d668",
                         "installed_by": ["modules"]
                     },
                     "bedtools/merge": {
                         "branch": "master",
-                        "git_sha": "9e51255c4f8ec69fb6ccf68593392835f14fecb8",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "custom/dumpsoftwareversions": {
                         "branch": "master",
-                        "git_sha": "76cc4938c1f6ea5c7d83fed1eeffc146787f9543",
+                        "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93",
                         "installed_by": ["modules"]
                     },
                     "gnu/sort": {
                         "branch": "master",
-                        "git_sha": "88f6e982fb8bd40488d837b3b08a65008e602840",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "minimap2/align": {
                         "branch": "master",
-                        "git_sha": "603ecbd9f45300c9788f197d2a15a005685b4220",
+                        "git_sha": "efbf86bb487f288ac30660282709d9620dd6048e",
                         "installed_by": ["modules"]
                     },
                     "minimap2/index": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "pretextmap": {
                         "branch": "master",
-                        "git_sha": "decfb802f2e573efb7b44ff06b11ecf16853054d",
+                        "git_sha": "6f4299292ef2c5b66e6829527b2647c301b77cc9",
                         "installed_by": ["modules"]
                     },
                     "pretextsnapshot": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "b119603b5ebefa3075cfa513d1d91b1dc875a679",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe",
+                        "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "0460d316170f75f323111b4a2c0a2989f0c32013",
+                        "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
                         "installed_by": ["modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
-                        "git_sha": "a0f7be95788366c1923171e358da7d049eb440f9",
+                        "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "3ffae3598260a99e8db3207dead9f73f87f90d1f",
+                        "git_sha": "ce0b1aed7d504883061e748f492a31bf44c5777c",
                         "installed_by": ["modules"]
                     },
                     "seqtk/cutn": {
                         "branch": "master",
-                        "git_sha": "726ee59cd9360a965d96ea9ea8770f16b8ddd6cc",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {
                         "branch": "master",
-                        "git_sha": "591b71642820933dcb3c954c934b397bd00d8e5e",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "ucsc/bedgraphtobigwig": {
                         "branch": "master",
-                        "git_sha": "66290981ab6038ea86177ade40b9449bc790b0ce",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "windowmasker/mkcounts": {
                         "branch": "master",
-                        "git_sha": "30c3ed32e8bd5ddaf349ba2f4f99d38182fdc08c",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     },
                     "windowmasker/ustat": {
                         "branch": "master",
-                        "git_sha": "726ee59cd9360a965d96ea9ea8770f16b8ddd6cc",
+                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
                         "installed_by": ["modules"]
                     }
                 }

diff --git a/modules/nf-core/bedtools/bamtobed/environment.yml b/modules/nf-core/bedtools/bamtobed/environment.yml
diff --git a/modules/nf-core/bedtools/bamtobed/main.nf b/modules/nf-core/bedtools/bamtobed/main.nf
diff --git a/modules/nf-core/bedtools/bamtobed/meta.yml b/modules/nf-core/bedtools/bamtobed/meta.yml
diff --git a/modules/nf-core/bedtools/bamtobed/tests/main.nf.test b/modules/nf-core/bedtools/bamtobed/tests/main.nf.test
diff --git a/modules/nf-core/bedtools/bamtobed/tests/main.nf.test.snap b/modules/nf-core/bedtools/bamtobed/tests/main.nf.test.snap
diff --git a/modules/nf-core/bedtools/bamtobed/tests/tags.yml b/modules/nf-core/bedtools/bamtobed/tests/tags.yml
diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml
diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf
diff --git a/modules/nf-core/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml