Filter empty FastQ files after adapter trimming

[svarona]

Description of feature

We suggest the introducction of a new checkpoint after fastp trimming simmilar to the one existing after the primer trimming:

viralrecon/workflows/illumina.nf

Line 218 in 42e38bb

pass = WorkflowIllumina.getFastpReadsAfterFiltering(json) > 0

to test wether the output trim.fastq.gz is empty or not. We could add it after this peace of code:

viralrecon/subworkflows/nf-core/fastqc_fastp.nf

Line 53 in 42e38bb

FASTQC_TRIM (

[poojasgupta]

I think I am facing a similar issue which might get fixed after addition of the feature request suggested by @svarona.
Sometimes, when my input fastq files are empty or very small due to failed sequencing or becomes empty after the fastp trimming step, the pipeline fails at the fastqc step. When this happens and I remove the failed sample, the pipeline completes successfully.
Here is the error message that I get.

Error executing process > 'NFCORE_VIRALRECON:ILLUMINA:FASTQC_FASTP:FASTQC_TRIM (220110_SDSDN16_UT_A01290_220117)'

Caused by:
  Process `NFCORE_VIRALRECON:ILLUMINA:FASTQC_FASTP:FASTQC_TRIM (220110_SDSDN16_UT_A01290_220117)` terminated with an error exit status (1)

Command executed:

  [ ! -f  220110_SDSDN16_UT_A01290_220117.fastq.gz ] && ln -s 220110_SDSDN16_UT_A01290_220117.trim.fastq.gz 220110_SDSDN16_UT_A01290_220117.fastq.gz
  fastqc --quiet --threads 6 220110_SDSDN16_UT_A01290_220117.fastq.gz
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_VIRALRECON:ILLUMINA:FASTQC_FASTP:FASTQC_TRIM":
      fastqc: $( fastqc --version | sed -e "s/FastQC v//g" )
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  Failed to process 220110_SDSDN16_UT_A01290_220117.fastq.gz
  java.io.EOFException
  	at java.base/java.util.zip.GZIPInputStream.readUByte(GZIPInputStream.java:269)
  	at java.base/java.util.zip.GZIPInputStream.readUShort(GZIPInputStream.java:259)
  	at java.base/java.util.zip.GZIPInputStream.readHeader(GZIPInputStream.java:165)
  	at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:80)
  	at java.base/java.util.zip.GZIPInputStream.(GZIPInputStream.java:92)
  	at uk.ac.babraham.FastQC.Utilities.MultiMemberGZIPInputStream.(MultiMemberGZIPInputStream.java:37)
  	at uk.ac.babraham.FastQC.Sequence.FastQFile.(FastQFile.java:80)
  	at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:106)
  	at uk.ac.babraham.FastQC.Sequence.SequenceFactory.getSequenceFile(SequenceFactory.java:62)
  	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:159)
  	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.(OfflineRunner.java:121)
  	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)

[drpatelh]

Fixed in a1f810b 6a0bc31