Merge pull request #21 from nf-core/igenomeParams

bwa and blacklist parameters names changes

README.md

@@ -90,21 +90,22 @@ For more details and further functionality, please refer to the [usage documenta
 
 ## Pipeline output
 
-To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/sammyseq/results) tab on the nf-core website pipeline page.
+<!-- TODO uncomment after first release: To see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/sammyseq/results) tab on the nf-core website pipeline page. -->
+
 For more details about the output files and reports, please refer to the
 [output documentation](https://nf-co.re/sammyseq/output).
 
 ## Credits
 
-nf-core/sammyseq was written by Margherita Mutarelli and Lucio Di Filippo and was based on the original pipeline developed _in-house_ by SAMMY-seq creators. <!-- TODO retreive all names and github usernames -->
+nf-core/sammyseq was written by Lucio Di Filippo and Margherita Mutarelli and was based on the original pipeline developed _in-house_ by SAMMY-seq creators. <!-- TODO retreive all names and github usernames -->
 
 We thank the following people for their extensive assistance in the development of this pipeline:
 
 <!-- TODO nf-core: If applicable, make list of people who have also contributed -->
 
 ## Acknowledgements
 
-The initial development of this pipeline was funded thanks to the projects Progetti@CNR Myo-CoV-2, AFM Téléthon EDMD-GenomeSCAN B53C22009260007 and PIR01_00011 I.Bi.S.Co. Infrastruttura per Big data e Scientific COmputing (PON 2014-2020).
+The development of this pipeline was made possible thanks to the projects Progetti@CNR Myo-CoV-2 B93C20046330005, AFM Téléthon EDMD-GenomeSCAN B53C22009260007 and PIR01_00011 I.Bi.S.Co. Infrastruttura per Big data e Scientific COmputing (PON 2014-2020).
 
 ## Contributions and Support
 
@@ -117,8 +118,6 @@ For further information or help, don't hesitate to get in touch on the [Slack `#
 <!-- TODO nf-core: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file. -->
 <!-- If you use  nf-core/sammyseq for your analysis, please cite it using the following doi: [10.5281/zenodo.XXXXXX](https://doi.org/10.5281/zenodo.XXXXXX) -->
 
-<!-- TODO nf-core: Add bibliography of tools and data used in your pipeline -->
-
 An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.
 
 You can cite the `nf-core` publication as follows:

conf/modules.config

@@ -144,10 +144,10 @@ process {
 
 }
 
-if (params.blackListFile != null) {
+if (params.blacklist != null) {
         process {
             withName: '.*DEEPTOOLS_BAMCOVERAGE.*' {
-                ext.args    = "–blackListFileName ${params.blackListFile}"
+                ext.args    = "–blackListFileName ${params.blacklist}"
             }
             }
 }

docs/usage.md

@@ -117,11 +117,11 @@ Optionally, the fractions extracted from the same `experimentalID` can be combin
 
 ## Reference genome files
 
-The minimum reference genome requirements is the FASTA file, provided with the mandatory parameter `--fasta`, the bwa index will be generated by the pipeline and can be saved for later reuse if the `--save_reference` parameter is passed. The index building step can be quite a time-consuming process and it permits their reuse for future runs of the pipeline to save disk space, if already present it can be passed using the `--bwa_index '/path/to/bwa/index/'` parameter.
+The minimum reference genome requirements is the FASTA file, provided with the mandatory parameter `--fasta`, the bwa index will be generated by the pipeline and can be saved for later reuse if the `--save_reference` parameter is passed. The index building step can be quite a time-consuming process and it permits their reuse for future runs of the pipeline to save disk space, if already present it can be passed using the `--bwa '/path/to/bwa/index/'` parameter.
 
 ### Blacklist bed files
 
-A blacklist of regions that will be excluded by signal tracks can be provided using the optional parameter `--blackListFile` with full path to a coordinate file in bed format. Blacklist files for several genome builds can be found in the [ENCODE Blacklist Project](https://github.com/Boyle-Lab/Blacklist).
+A blacklist of regions that will be excluded by signal tracks can be provided using the optional parameter `--blacklist` with full path to a coordinate file in bed format. Blacklist files for several genome builds can be found in the [ENCODE Blacklist Project](https://github.com/Boyle-Lab/Blacklist).
 
 ## Updating the pipeline
 

nextflow.config

@@ -17,7 +17,7 @@ params {
     genome                     = null
     igenomes_base              = 's3://ngi-igenomes/igenomes'
     igenomes_ignore            = true
-    bwa_index                  = null
+    bwa                  = null
     save_reference             = false
 
     //overall analysis options
@@ -32,7 +32,7 @@ params {
     multiqc_methods_description = null
 
     // bam generation
-    blackListFile              = null
+    blacklist                  = null
 
     // Boilerplate options
     outdir                     = null

nextflow_schema.json

@@ -98,7 +98,7 @@
                     "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
                     "fa_icon": "far fa-file-code"
                 },
-                "bwa_index": {
+                "bwa": {
                     "type": "string",
                     "format": "path",
                     "exists": true,
@@ -119,7 +119,7 @@
                     "default": true,
                     "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`. You can run `sammyseq` by specifying at least a FASTA genome file."
                 },
-                "blackListFile": {
+                "blacklist": {
                     "type": "string",
                     "format": "file-path",
                     "fa_icon": "fas fa-ban",

workflows/sammyseq.nf

@@ -100,7 +100,7 @@ workflow SAMMYSEQ {
 
 
     PREPARE_GENOME (params.fasta,
-                    params.bwa_index)
+                    params.bwa)
 
     ch_versions = ch_versions.mix(PREPARE_GENOME.out.versions)