Merge pull request #86 from KevinMenden/dev

cleaned up parameters

CHANGELOG.md

@@ -36,6 +36,7 @@ This release contains several major (potentially breaking) changes:
 * Add `--mirtrace_protocol` parameter to allow for more flexible selection of this parameter
 * Added `--trim_galore_max_length` option [[#77](https://github.com/nf-core/smrnaseq/issues/77)]
 * Solved memory usage issue for mirtrace in the main process and in the `get_software_versions` process [[#68](https://github.com/nf-core/smrnaseq/issues/68)]
+* Removed logging of `single_end` parameter and added missing parameters to schema and config files
 
 ### Packaged software updates
 

environment.yml

@@ -15,20 +15,20 @@ dependencies:
   - conda-forge::python=3.7.3
   - conda-forge::markdown=3.1.1
   - conda-forge::pymdown-extensions=6.0
-  - conda-forge::pygments=2.6.1
-  - conda-forge::pigz=2.3.4
+  - conda-forge::pygments=2.9.0
+  - conda-forge::pigz=2.6
 
   # bioconda packages
   - bioconda::fastqc=0.11.9
-  - bioconda::trim-galore=0.6.5
-  - bioconda::samtools=1.9
-  - bioconda::bowtie=1.2.3
-  - bioconda::multiqc=1.9
+  - bioconda::trim-galore=0.6.6
+  - bioconda::samtools=1.12
+  - bioconda::bowtie=1.3.0
+  - bioconda::multiqc=1.10.1
   - bioconda::mirtop=0.4.23
   - bioconda::seqcluster=1.2.7
-  - bioconda::htseq=0.11.3
+  - bioconda::htseq=0.13.5
   - bioconda::fastx_toolkit=0.0.14
-  - bioconda::seqkit=0.12.0
+  - bioconda::seqkit=0.16.0
   - bioconda::mirtrace=1.0.1
   - bioconda::bioconductor-edger=3.26.5
   - bioconda::bioconductor-limma=3.40.2

main.nf

@@ -181,7 +181,6 @@ summary['Current path']        = "$PWD"
 summary['Script dir']          = workflow.projectDir
 summary['Config Profile']      = (workflow.profile == 'standard' ? 'UPPMAX' : workflow.profile)
 summary['Fasta Ref']        = params.fasta
-summary['Data Type']        = params.single_end ? 'Single-End' : 'Paired-End'
 summary['Max Resources']    = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job"
 if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container"
 summary['Output dir']       = params.outdir

nextflow.config

@@ -15,10 +15,12 @@ params {
   protocol = 'illumina'
 
   // Reference genomes
-  genome = false
-  mirna_gtf = false
-  fasta = false
-  bt_index = false
+  genome = null
+  gtf = null
+  mirna_gtf = null
+  fasta = null
+  bt_index = null
+  bt_indices = null
   mirtrace_species = false
   mirtrace_protocol = false
   references_parsed = false

nextflow_schema.json

@@ -122,6 +122,15 @@
                     "fa_icon": "fas fa-ban",
                     "hidden": 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`."
+                },
+                "gtf": {
+                    "type": "string",
+                    "description": "Path to reference genome GTF file",
+                    "fa_icon": "fas fa-address-book"
+                },
+                "bt_indices": {
+                    "type": "array",
+                    "description": "List of bowtie index files"
                 }
             }
         },