Put trim and multiqc rules into one group.

This ensures that for remote execution these rules share the same
nodes, which works around missing input declarations for the multiqc
rule.

snakefile.py

@@ -331,6 +331,7 @@ def trim_reads_input(args):
     r2=os.path.join(TRIMMED_READS_DIR, "{sample}.trimmed.R2.fq.gz"),
     html=os.path.join(QC_DIR, "{sample}.pe.fastp.html"),
     json=os.path.join(QC_DIR, "{sample}.pe.fastp.json") #notice that multiqc recognizes files ending with fast.json
+  group: "qc"
   resources:
     mem_mb = config['execution']['rules']['trim_qc_reads_pe']['memory']
   log: os.path.join(LOG_DIR, 'trim_reads.{sample}.log')
@@ -343,6 +344,7 @@ def trim_reads_input(args):
     r = os.path.join(TRIMMED_READS_DIR, "{sample}.trimmed.fq.gz"),
     html=os.path.join(QC_DIR, "{sample}.se.fastp.html"),
     json=os.path.join(QC_DIR, "{sample}.se.fastp.json") #notice that multiqc recognizes files ending with fast.json
+  group: "qc"
   resources:
     mem_mb = config['execution']['rules']['trim_qc_reads_se']['memory']
   log: os.path.join(LOG_DIR, 'trim_reads.{sample}.log')
@@ -553,6 +555,7 @@ def hisat2_file_arguments(args):
   input:
     salmon_output=expand(os.path.join(SALMON_DIR, "{sample}", "quant.sf"), sample = SAMPLES),
     mapping_output=expand(os.path.join(MAPPED_READS_DIR, MAPPER, '{sample}_Aligned.sortedByCoord.out.bam'), sample=SAMPLES)
+  group: "qc"
   output: os.path.join(MULTIQC_DIR, 'multiqc_report.html')
   resources:
     mem_mb = config['execution']['rules']['multiqc']['memory']