Merge pull request #2 from asp8200/dev

Dev

CHANGELOG.md

@@ -23,11 +23,21 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#681](https://github.com/nf-core/sarek/pull/681) - Fixed intermediate files published cf [#680](https://github.com/nf-core/sarek/issues/680)
 - [#688](https://github.com/nf-core/sarek/pull/688) - Fixed VEP plugins issue cf [#687](https://github.com/nf-core/sarek/issues/687)
 - [#689](https://github.com/nf-core/sarek/pull/689) - Fixed when clause for non `BWA mem` building mapping indexes
+- [#704](https://github.com/nf-core/sarek/pull/704) - Fixed `cf_ploidy` to string instead of number
+- [#706](https://github.com/nf-core/sarek/pull/706) - Fixed `vep_version` not found error when running `--vep_loftee`
 
 ### Deprecated
 
 ### Removed
 
+## [3.0.1](https://github.com/nf-core/sarek/releases/tag/3.0.1) - Saiva
+
+Saiva is a lake in the Sarek national park, just below the Skierfe mountain.
+
+### Fixed
+
+- [#708](https://github.com/nf-core/sarek/pull/708) - Fixes mpileup bug. Update nf-core module `samtools/mpileup` to subset CRAM file by intervals.
+
 ## [3.0](https://github.com/nf-core/sarek/releases/tag/3.0) - Skierfe
 
 Skierfe is a mountain in the Sarek national park, and the inspiration for the logo.

conf/modules.config

@@ -1208,15 +1208,15 @@ process{
     // VEP
     if (params.tools && (params.tools.split(',').contains('vep') || params.tools.split(',').contains('merge'))) {
         withName: 'ENSEMBLVEP' {
-            ext.args          = [
+            ext.args          = { [
                 '--everything --filter_common --per_gene --total_length --offline --format vcf',
                 (params.vep_dbnsfp && params.dbnsfp && !params.dbnsfp_consequence)    ? "--plugin dbNSFP,${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"                                              : '',
                 (params.vep_dbnsfp && params.dbnsfp && params.dbnsfp_consequence)     ? "--plugin dbNSFP,'consequence=${params.dbnsfp_consequence}',${params.dbnsfp.split("/")[-1]},${params.dbnsfp_fields}"   : '',
                 (params.vep_loftee)                                                   ? "--plugin LoF,loftee_path:/opt/conda/envs/nf-core-vep-${params.vep_version}/share/ensembl-vep-${params.vep_version}-0" : '',
                 (params.vep_spliceai && params.spliceai_snv && params.spliceai_indel) ? "--plugin SpliceAI,snv=${params.spliceai_snv.split("/")[-1]},indel=${params.spliceai_indel.split("/")[-1]}"            : '',
                 (params.vep_spliceregion)                                             ? '--plugin SpliceRegion'                                                                                                : '',
                 (params.vep_out_format)                                               ? "--${params.vep_out_format}"                                                                                           : '--vcf'
-            ].join(' ').trim()
+            ].join(' ').trim() }
             // If just VEP: <vcf prefix>_VEP.ann.vcf
             ext.prefix       = { "${vcf.baseName.minus(".vcf")}_VEP" }
             if (!params.vep_cache)    container = { params.vep_genome ? "nfcore/vep:${params.vep_version}.${params.vep_genome}" : "nfcore/vep:${params.vep_version}.${params.genome}" }

docs/output.md

@@ -249,7 +249,7 @@ See the [`--input`](usage.md#--input) section in the usage documentation for fur
 ## Variant Calling
 
 The results regarding variant calling are collected in `{outdir}/variantcalling/`.
-If some results from a variant caller do not appear here, please check out the `--tools` section in the parameter [documentation](https://nf-co.re/sarek/3.0.0/parameters).
+If some results from a variant caller do not appear here, please check out the `--tools` section in the parameter [documentation](https://nf-co.re/sarek/3.0.1/parameters).
 
 (Recalibrated) CRAM files can used as an input to start the variant calling.
 

docs/usage.md

@@ -300,8 +300,8 @@ nextflow pull nf-core/sarek
 
 It is a good idea to specify a pipeline version when running the pipeline on your data. This ensures that a specific version of the pipeline code and software are used when you run your pipeline. If you keep using the same tag, you'll be running the same version of the pipeline, even if there have been changes to the code since.
 
-First, go to the [nf-core/sarek releases page](https://github.com/nf-core/sarek/releases) and find the latest version number - numeric only (eg. `3.0.0`).
-Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 3.0.0`.
+First, go to the [nf-core/sarek releases page](https://github.com/nf-core/sarek/releases) and find the latest version number - numeric only (eg. `3.0.1`).
+Then specify this when running the pipeline with `-r` (one hyphen) - eg. `-r 3.0.1`.
 
 This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future.
 
@@ -483,7 +483,7 @@ If you have any questions or issues please send us a message on [Slack](https://
 When using default parameters only, sarek runs preprocessing and exits after base quality score recalibration. This is reflected in the default test profile:
 
 ```console
-nextflow run nf-core/sarek -r 3.0 -profile test,<container/institute>
+nextflow run nf-core/sarek -r 3.0.1 -profile test,<container/institute>
 ```
 
 Expected run output:
@@ -533,13 +533,13 @@ Expected run output:
 The pipeline comes with a number of possible paths and tools that can be used. The easiest and fastest test to see that the preprocessing + variantcalling (in this case Strelka2) works, is to run:
 
 ```console
-nextflow run nf-core/sarek -r 3.0.0 -profile test,<container/institute> --tools strelka
+nextflow run nf-core/sarek -r 3.0.1 -profile test,<container/institute> --tools strelka
 ```
 
 Due to the small test data size, unfortunately not everything can be tested from top-to-bottom, but often is done by utilizing the pipeline's `--step` parameter. Annotation has to tested separatly from the remaining workflow, since we use references for `C.elegans`, while the remaining tests are run on downsampled human data.
 
 ```console
-nextflow run nf-core/sarek -r 3.0.0 -profile test,<container/institute> --tools snpeff --step annotation
+nextflow run nf-core/sarek -r 3.0.1 -profile test,<container/institute> --tools snpeff --step annotation
 ```
 
 If you are interested in any of the other tests that are run on every code change or would like to run them yourself, you can take a look at `tests/<filename>.yml`. For each entry the respective nextflow command run and the expected output is specified.
@@ -809,4 +809,4 @@ ERROR_CHROMOSOME_NOT_FOUND      17522411
 
 ## How to set up sarek to use sentieon
 
-Sarek 3.0 is currently not supporting sentieon. It is planned for the upcoming release 3.1. In the meantime, please revert to the last release 2.7.2.
+Sarek 3.0.1 is currently not supporting sentieon. It is planned for the upcoming release 3.1. In the meantime, please revert to the last release 2.7.2.

modules.json

@@ -205,7 +205,7 @@
                 "git_sha": "720027275ccdc1363bb2a19c6412da148e31d94b"
             },
             "samtools/mpileup": {
-                "git_sha": "24e05f6097a5dde57dd80d33295ed120f1b81aef"
+                "git_sha": "454e0acc09de7cdcc90007420bfe8afa251286fb"
             },
             "samtools/stats": {
                 "git_sha": "f48a24770e24358e58de66e9b805a70d77cd154b"

nextflow.config

@@ -55,7 +55,7 @@ params {
     ascat_min_counts = 10               // default value for ASCAT
     ascat_min_map_qual = 35             // default value for ASCAT
     ascat_purity = null                 // default value for ASCAT
-    cf_ploidy = 2                       // default value for Control-FREEC
+    cf_ploidy = "2"                     // default value for Control-FREEC
     cf_coeff = 0.05                     // default value for Control-FREEC
     cf_contamination = 0                // default value for Control-FREEC
     cf_contamination_adjustment = false // by default we are not using this in Control-FREEC
@@ -101,7 +101,7 @@ params {
     help                       = false
     validate_params            = true
     show_hidden_params         = false
-    schema_ignore_params       = 'genomes,snpeff_version,vep_version'
+    schema_ignore_params       = 'genomes,snpeff_version,vep_version,cf_ploidy'
     enable_conda               = false
 
     // Config options

nextflow_schema.json

@@ -316,8 +316,8 @@
                     "help_text": "Details, see [ControlFREEC manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html)."
                 },
                 "cf_ploidy": {
-                    "type": "integer",
-                    "default": 2,
+                    "type": "string",
+                    "default": "2",
                     "fa_icon": "fas fa-bacon",
                     "help_text": "In case of doubt, you can set different values and Control-FREEC will select the one that explains most observed CNAs Example: ploidy=2 , ploidy=2,3,4. For more details, see the [manual](http://boevalab.inf.ethz.ch/FREEC/tutorial.html).",
                     "description": "Genome ploidy used by ControlFREEC",