Update multiqc to version 1.4 (#389)

*  update multiqc

*  update typos in the documentation

CGATPipelines/pipeline_mapping.py

@@ -74,7 +74,7 @@
 fastq.gz
    Single-end reads in fastq format.
 
-fastq.1.gz, fastq2.2.gz
+fastq.1.gz, fastq.2.gz
    Paired-end reads in fastq format. The two fastq files must be
    sorted by read-pair.
 

CGATPipelines/pipeline_readqc.py

@@ -68,7 +68,7 @@
 fastq.gz
    Single-end reads in fastq format.
 
-fastq.1.gz, fastq2.2.gz
+fastq.1.gz, fastq.2.gz
    Paired-end reads in fastq format.
    The two fastq files must be sorted by read-pair.
 

CGATPipelines/pipeline_rnaseqqc.py

@@ -57,7 +57,7 @@
 fastq.gz
    Single-end reads in fastq format.
 
-fastq.1.gz, fastq2.2.gz
+fastq.1.gz, fastq.2.gz
    Paired-end reads in fastq format.
    The two fastq files must be sorted by read-pair.
 

conda/environments/pipelines-extra.yml

@@ -14,4 +14,4 @@ dependencies:
 - blast=2.7.1
 - bashlex=0.12
 - pandoc=1.19.2
-- multiqc=1.3
+- multiqc=1.4

scripts/cgat_tsv2links.py

@@ -9,8 +9,8 @@
 columns, for example::
 
    source     dest
-   abc.fq.gz  sample1-R1.fq.gz
-   def.fq.gz  sample1-R2.fq.gz
+   abc.fq.gz  sample1-condition-R1.fastq.1.gz
+   def.fq.gz  sample1-condition-R2.fastq.2.gz
 
 If the options ``--source`` is given, filenams will be matched by
 walking through ``--source``. Otherwise, filenames in the source