Merge pull request #699 from drpatelh/updates

Fix #690 and #697

CHANGELOG.md

@@ -8,6 +8,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Enhancements & fixes
 
 * Add `python3` shebang to appropriate scripts in `bin/` directory
+* [[#690](https://github.com/nf-core/rnaseq/issues/690)] - Error with post-trimmed read 2 sample names from FastQC in MultiQC
+* [[#697](https://github.com/nf-core/rnaseq/issues/697)] - pipeline_report.{txt,html} missing from pipeline_info directory
 
 ### Parameters
 

assets/multiqc_config.yaml

@@ -54,13 +54,12 @@ report_section_order:
 
 # Don't show % Dups in the General Stats table (we have this from Picard)
 table_columns_visible:
-    FastQC:
+    fastqc:
         percent_duplicates: False
 
 extra_fn_clean_exts:
     - '.umi_dedup'
-    - '_2_val_2'
-    - '_val_1'
+    - '_val'
 
 # Customise the module search patterns to speed up execution time
 #  - Skip module sub-tools that we are not interested in

conf/modules.config

@@ -22,26 +22,6 @@
 
 params {
     modules {
-        'sra_ids_to_runinfo' {
-            publish_dir     = 'public_data'
-            publish_files   = ['tsv':'runinfo']
-        }
-        'sra_runinfo_to_ftp' {
-            publish_dir     = 'public_data'
-            publish_files   = ['tsv':'runinfo']
-        }
-        'sra_fastq_ftp' {
-            publish_dir     = 'public_data'
-            publish_files   = ['fastq.gz':'', 'md5':'md5']
-            args            = '-C - --max-time 1200'
-        }
-        'sra_to_samplesheet' {
-            publish_dir     = 'public_data'
-            publish_files   = false
-        }
-        'sra_merge_samplesheet' {
-            publish_dir     = 'public_data'
-        }
         'gffread' {
             args            = '--keep-exon-attrs -F -T'
             publish_dir     = 'genome'

docs/output.md

@@ -674,7 +674,7 @@ A number of genome-specific files are generated by the pipeline because they are
 
 * `pipeline_info/`
     * Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`.
-    * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.tsv`.
+    * Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.tsv`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline.
     * Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`.
 
 </details>