Merge pull request #35 from cokelaer/main

Fix Annotation plot, add new expression plot

README.rst

@@ -158,6 +158,8 @@ Changelog
 ========= ====================================================================
 Version   Description
 ========= ====================================================================
+0.18.1    * fastp multiqc regression. Fixed missing sample names by updating
+            multiqc_config and adding sample names in the output filename
 0.18.0    * New plots in the HTML reports. Includes version of executables.
 0.17.2    * CHANGES: in star section, added --limitBAMsortRAM and set to 30G
           * BUG: Fix missing params (options) in star_mapping rule not taken

requirements.txt

@@ -1,4 +1,4 @@
-sequana>=0.14.2
-sequana_pipetools>=0.9.2
+sequana>=0.15.4
+sequana_pipetools>=0.14.0
 cutadapt
 atropos

sequana_pipelines/rnaseq/multiqc_config.yaml

@@ -115,7 +115,8 @@ sp:
         fn: '*Log.final.out'
     cutadapt:
         fn: 'cutadapt.txt'
-
+    fastp:
+        fn: '*fastp*json'
     #rna_seqc/metrics:
     #    fn: "*metrics.tsv"
     #rna_seqc/coverage:

sequana_pipelines/rnaseq/rnaseq.rules

@@ -370,8 +370,8 @@ elif manager.config.trimming.software_choice == "fastp":
             sample=manager.getrawdata()
         output:
             trimmed=__clean_fastq__output,
-            html="{sample}/fastp/fastp.html",
-            json="{sample}/fastp/fastp.json", # must be named fastp
+            html="{sample}/fastp/fastp_{sample}.html",
+            json="{sample}/fastp/fastp_{sample}.json", # must be named fastp
         log:
             "logs/fastp/{sample}.log"
         params:

setup.py

@@ -5,7 +5,7 @@
 
 _MAJOR = 0
 _MINOR = 18
-_MICRO = 0
+_MICRO = 1
 version = "%d.%d.%d" % (_MAJOR, _MINOR, _MICRO)
 release = "%d.%d" % (_MAJOR, _MINOR)