remove unnecessary file

rules/merge_samples.smk

-'''
-Author: Monica R. Ticlla
-Afiliation(s): SIB, SwissTPH, UNIBAS
-Description: after pre-processing of paired fastq files form paired-end shotgun
-DNA sequencing of metagenomic samples, fastq files corresponding to the same
-sample are merged into a single pair of fastq files.
-
-'''
-localrules:
-    multiqc_merged_list_files,
-    multiqc_merged
-##----------------------------------------------------------------------------##
-## Local variables
-##----------------------------------------------------------------------------##
-singularity_img = 'shub://mticlla/MetagenomicSnake:preqc_v0_1'
-
-##----------------------------------------------------------------------------##
-## Rules with target files
-##----------------------------------------------------------------------------##
-
-###**THESE TARGET FILES ARE THE FINAL CLEAN**###
-# concatenate cleaned,deduplicated and trimmed fastqs from the same samples
-rule concatenate_fastqs:
-    input:
-        #
-        sample_fwds = lambda wildcards: ['{}/{}_dfinaltrim/{}-{}_{}-R1.clean.nodup.fastp.fastq.gz'.format(
-        PRE_PROC_DIR, DATASETS[ix], value, RUNS[ix], LANES[ix])
-        for ix,value in enumerate(SAMPLES) if (value == wildcards.sample) and (DATASETS[ix] == wildcards.dataset)],
-        #
-        sample_revs = lambda wildcards: ['{}/{}_dfinaltrim/{}-{}_{}-R2.clean.nodup.fastp.fastq.gz'.format(
-        PRE_PROC_DIR, DATASETS[ix], value, RUNS[ix], LANES[ix])
-        for ix,value in enumerate(SAMPLES) if (value==wildcards.sample) and (DATASETS[ix]==wildcards.dataset)]
-    output:
-        sample_fwd = MERGE_DIR + '/{dataset}_merged/{sample}-R1.fastq.gz',
-        sample_rev = MERGE_DIR + '/{dataset}_merged/{sample}-R2.fastq.gz'
-    wildcard_constraints:
-        sample = '\w+'
-    group: 'preprocess'
-    shell:
-        '''
-        cat {input.sample_fwds} > {output.sample_fwd}
-        cat {input.sample_revs} > {output.sample_rev}
-        '''
-# Final quality check with Fastp, but no further QC processing
-rule fastp_concatenated:
-    input:
-        sample_fwd = MERGE_DIR + '/{dataset}_merged/{sample}-R1.fastq.gz',
-        sample_rev = MERGE_DIR + '/{dataset}_merged/{sample}-R2.fastq.gz'
-    output:
-        report1 = MERGE_DIR + '/{dataset}_merged/{sample}.fastp.html',
-        report2 = MERGE_DIR + '/{dataset}_merged/{sample}.fastp.json'
-    wildcard_constraints:
-        sample = '\w+'
-    threads: cpus_avail
-    group: 'preprocess'
-    singularity: singularity_img
-    shell:
-        '''
-        fastp \
-        -A \
-        --in1 {input.sample_fwd} --in2 {input.sample_rev} \
-        --html {output.report1} --json {output.report2} \
-        --thread {threads}
-        '''
-
-rule multiqc_merged_list_files:
-    input:
-        sample_fastp_report = lambda wildcards: ['{}/{}_merged/{}.fastp.json'.format(
-        MERGE_DIR, wildcards.dataset, value) for ix,value in enumerate(SAMPLES)
-        if DATASETS[ix]==wildcards.dataset]
-    output:
-        multiqc_input_list = MERGE_REPORT + '/{dataset}_multiqc_inputs.txt'
-    run:
-        import os
-        try:
-            os.makedirs(os.path.dirname(output.multiqc_input_list))
-        except OSError:
-            pass
-
-        with open(output.multiqc_input_list, mode='w', encoding='utf-8') as out:
-            for item in set(input.sample_fastp_report):
-                out.write("%s\n" % item)
-rule multiqc_merged:
-    input:
-        MERGE_REPORT + '/{dataset}_multiqc_inputs.txt'
-    output:
-        multiqc_report=report(MERGE_REPORT + '/{dataset}_multiqc.html',
-        category='merge_samples')
-    singularity: singularity_img
-    shell:
-        '''
-        multiqc -f --file-list {input} --filename {output.multiqc_report}
-        '''