Correct versioning information in modules

sanger-tol · Dec 9, 2024 · 55756f1 · 55756f1
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,68 @@
 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).
 
+
+## [[1.1.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.1.0)] - UNSC Delphi - [2024-12-09]
+
+### Added
+
+- Added map_order so that the output maps are defaulted to unsorted and can be selected as sorted.
+- Updating all modules.
+- Removing Anaconda 'defaults' channel.
+- Updating local module containers.
+- Update to LISCENSES and CITATIONS files.
+- Update algorithms at play for memory allocation, particulary minimap2.
+- Parity update to TreeVal as the mapping subworkflow is based on the treeval implementation.
+
+### Paramters
+
+| Old Version | New Versions    |
+| -           | --map_order     |
+
+### 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   |
+| ------------------------------------------------------------------- | -------------- | -------------- |
+| get_avcov | - | 1.0.0 |
+| bamtobed_sort ( bedtools + samtools )                               | 2.31.0 + 1.17              | 2.31.1 + 1.17  |
+| bedtools ( all modules) | 2.31.1         | -         |
+| bwamem2 index                                                       | -              | 2.2.1          |
+| cram_filter_align_bwamem2_fixmate_sort                              | -              |                |
+| ^ ( samtools + bwamem2 ) ^                                          | 1.17 + 2.2.1 | -   |
+| cram_filter_minimap2_filter5end_fixmate_sort                        | -              |                |
+| custom_dumpsoftwareversions | - | Python 3.11.7 + yaml 5.4.1 |
+| ^ ( samtools + minimap2 ) ^                                         | 1.17 + 2.24              |  -   |
+| extract_cov_id ( coreutils )                                        | 9.1              | 9.3            |
+| extract_repeat ( perl )                                             | 5.26.2              | -         |
+| extract_telo ( coreutils )                                          | -              | 9.1            |
+| find_telomere_regions ( gcc )                                       | 7.1.0         | 7.1.0 + 1.0         |
+| find_telomere_windows ( java-jdk )                                  | 8.0.112              | 8.0.112 + 1.0       |
+| findhalfcoverage ( python )                                  | -              | 3.9.1 + 1.0       |
+| gap_length ( coreutils )                                            | 9.1              | 9.3            |
+| generate_cram_csv ( samtools )                                      | 1.17              | -           |
+| get_largest_scaff ( coreutils )                                     | 9.1              | -            |
+| getminmaxpunches ( coreutils )                                     | 9.1              | -            |
+| graphoverallcoverage ( perl )                                     | -              | 5.26.2 + 1.0            |
+| gnu-sort                                                            | 8.25              | 9.3           |
+| longreadcoveragescalelog | - | Python 3.9.1 + 1.0 |
+| minimap2 + samtools (align, map) | | 2.28-r1209 + 1.20
+| pretextmap + samtools                                               | 0.1.9 + 1.18   | 0.1.9\* + 1.20 |
+| pretextgraph                                                        |0.0.4                | 0.0.6          |
+| pretextsnapshot + UCSC                                              | 0.0.6b + 447    | 0.0.4 (official version)   |
+| rename_ids ( coreutils ) | - | 9.1 |
+| replace_dots ( coreutils ) | - | 9.1 |
+| seqtk                                                               | 1.4              | 1.4-r122            |
+| samtools (faidx,merge,sort,view)                                    | 1.18           | 1.21           |
+| ucsc                                                                | 445            | 469            |
+| windowmasker (blast)                                                | 2.14.0 + 1.0.0              | -       |
+
+Even modules which have not had a version bump have indeed been updated through NF-core to remove defaults.
+
+Some modules now have two verions, the new addition is the script version rather than just the dependency version.
+
+
 ## [[1.0.0](https://github.com/sanger-tol/curationpretext/releases/tag/1.0.0)] - UNSC Cradle - [2024-02-22]
 
 ### Added

diff --git a/bin/get_avgcov.sh b/bin/get_avgcov.sh
@@ -6,6 +6,7 @@
 # into bed format for use
 # -------------------
 # Author = yy5
+# Modified = dp24
 # -------------------
 version='1.0.0'
 if [ $1 == '-v' ];

diff --git a/modules/local/extract_repeat.nf b/modules/local/extract_repeat.nf
@@ -25,7 +25,7 @@ process EXTRACT_REPEAT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | awk '/This/ {print \$9}') | tr -d ())
+        perl: \$(echo \$(perl --version 2>&1) | awk '/This/ {print \$9}'))
         extract_repeat.pl: $VERSION
     END_VERSIONS
     """
@@ -38,7 +38,7 @@ process EXTRACT_REPEAT {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | awk '/This/ {print \$9}') | tr -d ())
+        perl: \$(echo \$(perl --version 2>&1) | awk '/This/ {print \$9}'))
         extract_repeat.pl: $VERSION
     END_VERSIONS
     """

diff --git a/modules/local/find_telomere_regions.nf b/modules/local/find_telomere_regions.nf
@@ -29,7 +29,7 @@ process FIND_TELOMERE_REGIONS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        find_telomere: \$(find_telomere -v)
+        find_telomere: \$(VERSION)
     END_VERSIONS
     """
 
@@ -42,7 +42,7 @@ process FIND_TELOMERE_REGIONS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        find_telomere: \$(find_telomere -v)
+        find_telomere: \$(VERSION)
     END_VERSIONS
     """
 

diff --git a/modules/local/graphoverallcoverage.nf b/modules/local/graphoverallcoverage.nf
@@ -25,7 +25,7 @@ process GRAPHOVERALLCOVERAGE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
+        perl: \$(echo \$(perl --version 2>&1) | awk '/This/ {print \$9}'))
         graph_overall_coverage.pl: \$(graph_overall_coverage.pl --version)
     END_VERSIONS
     """
@@ -37,8 +37,7 @@ process GRAPHOVERALLCOVERAGE {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        perl: \$(echo \$(perl --version 2>&1) | sed 's/^.*perl //; s/Using.*\$//')
-        graph_overall_coverage.pl: \$(graph_overall_coverage.pl --version)
+        perl: \$(echo \$(perl --version 2>&1) | awk '/This/ {print \$9}'))        graph_overall_coverage.pl: \$(graph_overall_coverage.pl --version)
     END_VERSIONS
     """
 }