Merge pull request #3 from avani-bhojwani/fix-linting

Linting and param updates

.nf-core.yml

@@ -1,2 +1,6 @@
 repository_type: pipeline
 nf_core_version: "2.14.1"
+lint:
+  nextflow_config:
+    - config_defaults:
+        - params.ribo_database_manifest

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/denovotranscript/tree/dev" target="_blank">nf-core/denovotranscript</a>
+  This report has been generated by the <a href="https://github.com/nf-core/denovotranscript/releases/tag/1.0.0" target="_blank">nf-core/denovotranscript</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/denovotranscript/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/denovotranscript/1.0.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-denovotranscript-methods-description":
     order: -1000

docs/usage.md

@@ -127,7 +127,7 @@ assemblers/methods/outputs to want to include as inputs to Evidential Gene:
 - `--soft_filtered_transcripts` (to include soft filtered transcripts from rnaSPAdes as inputs to Evidential Gene)
 - `--hard_filtered_transcripts` (to include hard filtered transcripts from rnaSPAdes as inputs to Evidential Gene)
 
-Extra parameters can be provided to Trinity using the `extra_trinity_args` parameter.
+Extra parameters can be provided to Trinity using the `extra_trinity_args` parameter. The `ss` param can be used to set the strand-specific type for rnaSPAdes.
 
 All assemblies are concatenated into one and redundancy is reduced using
 Evidential Gene's tr2aacds tool. You can provide additional parameters to tr2aacds
@@ -150,7 +150,7 @@ You can provide the path to the transcriptome assembly fasta file with the `--tr
 The typical command for running the pipeline is as follows:
 
 ```bash
-nextflow run nf-core/denovotranscript --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker
+nextflow run nf-core/denovotranscript --input ./samplesheet.csv --outdir ./results -profile docker
 ```
 
 This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles.
@@ -183,7 +183,6 @@ with `params.yaml` containing:
 ```yaml
 input: './samplesheet.csv'
 outdir: './results/'
-genome: 'GRCh37'
 <...>
 ```
 

modules.json

@@ -27,9 +27,8 @@
                     },
                     "fastp": {
                         "branch": "master",
-                        "git_sha": "b90b5cd93149a1b3be263d916c7234fe0708a71c",
-                        "installed_by": ["fastq_trim_fastp_fastqc"],
-                        "patch": "modules/nf-core/fastp/fastp.diff"
+                        "git_sha": "95cf5fe0194c7bf5cb0e3027a2eb7e7c89385080",
+                        "installed_by": ["fastq_trim_fastp_fastqc", "modules"]
                     },
                     "fastqc": {
                         "branch": "master",