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move renamePE to own template.
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bowtie2 and retrieve mapped reads now work for SE
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@cimendes
cimendes committed Oct 15, 2019
1 parent e58f2cc commit f69f735
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Showing 4 changed files with 315 additions and 167 deletions.
100 changes: 74 additions & 26 deletions DEN-IM.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -400,7 +400,7 @@ file ".versions"
then
prinseq-lite.pl --fastq ${sample_id}_1.fq --fastq2 ${sample_id}_2.fq --custom_params "${adapter}" -out_format 3 -out_good ${sample_id}_filtered
else
prinseq-lite.pl --fastq ${sample_id}_1.fq --custom_params "${adapter}" -out_format 3 -out_good ${sample_id}_filtered
prinseq-lite.pl --fastq ${sample_id}.fq --custom_params "${adapter}" -out_format 3 -out_good ${sample_id}_filtered
fi
gzip ${sample_id}_filtered*
Expand Down Expand Up @@ -492,7 +492,7 @@ process bowtie_1_4 {
each file(index_files) from bowtieIndex_1_4

output:
set sample_id , file("*.bam") into bowtie_out_1_3
set sample_id , file("pair_info.txt"), file("*.bam") into bowtie_out_1_3
set sample_id, file("*_bowtie2.log") into into_json_1_4
set sample_id, val("1_4_bowtie"), file(".status"), file(".warning"), file(".fail"), file(".command.log") into STATUS_bowtie_1_4
set sample_id, val("bowtie_1_4"), val("1_4"), file(".report.json"), file(".versions"), file(".command.trace") into REPORT_bowtie_1_4
Expand All @@ -501,19 +501,39 @@ file ".versions"
script:
"""
{
bowtie2 -x $index -1 ${fastq_pair[0]} -2 ${fastq_pair[1]} -p $task.cpus 1> ${sample_id}.bam 2> ${sample_id}_bowtie2.log
a=(${fastq_pair})
if [ "$clear" = "true" ];
if ((\${#a[@]} > 1));
then
work_regex=".*/work/.{2}/.{30}/.*"
file_source1=\$(readlink -f \$(pwd)/${fastq_pair[0]})
file_source2=\$(readlink -f \$(pwd)/${fastq_pair[1]})
if [[ "\$file_source1" =~ \$work_regex ]]; then
rm \$file_source1 \$file_source2
echo "True" > pair_info.txt
bowtie2 -x $index -1 ${fastq_pair[0]} -2 ${fastq_pair[1]} -p $task.cpus 1> ${sample_id}.bam 2> ${sample_id}_bowtie2.log
if [ "$clear" = "true" ];
then
work_regex=".*/work/.{2}/.{30}/.*"
file_source1=\$(readlink -f \$(pwd)/${fastq_pair[0]})
file_source2=\$(readlink -f \$(pwd)/${fastq_pair[1]})
if [[ "\$file_source1" =~ \$work_regex ]]; then
rm \$file_source1 \$file_source2
fi
fi
fi
echo pass > .status
echo pass > .status
else
echo "False" > pair_info.txt
bowtie2 -x $index -U ${fastq_pair[0]} -p $task.cpus 1> ${sample_id}.bam 2> ${sample_id}_bowtie2.log
if [ "$clear" = "true" ];
then
work_regex=".*/work/.{2}/.{30}/.*"
file_source1=\$(readlink -f \$(pwd)/${fastq_pair[0]})
if [[ "\$file_source1" =~ \$work_regex ]]; then
rm \$file_source1
fi
fi
echo pass > .status
fi
} || {
echo fail > .status
}
Expand Down Expand Up @@ -549,7 +569,7 @@ file ".versions"
process retrieve_mapped_1_5 {

// Send POST request to platform
if ( params.platformHTTP != null ) {
if ( params.platformHTTP != null ) {
beforeScript "PATH=${workflow.projectDir}/bin:\$PATH; export PATH; set_dotfiles.sh; startup_POST.sh $params.projectId $params.pipelineId 1_5 $params.platformHTTP"
afterScript "final_POST.sh $params.projectId $params.pipelineId 1_5 $params.platformHTTP; report_POST.sh $params.projectId $params.pipelineId 1_5 $params.sampleName $params.reportHTTP $params.currentUserName $params.currentUserId retrieve_mapped_1_5 \"$params.platformSpecies\" true"
} else {
Expand All @@ -560,32 +580,60 @@ process retrieve_mapped_1_5 {
publishDir 'results/mapping/retrieve_mapped_1_5/'

input:
set sample_id, file(bam) from bowtie_out_1_3
set sample_id, file(is_pair), file(bam) from bowtie_out_1_3

output:
set sample_id , file("*.headersRenamed_*.fq.gz") into retrieve_mapped_out_1_4
set sample_id , file("*_mapped*") into OUT_retrieve_mapped_1_4
set sample_id, val("1_5_retrieve_mapped"), file(".status"), file(".warning"), file(".fail"), file(".command.log") into STATUS_retrieve_mapped_1_5
set sample_id, val("retrieve_mapped_1_5"), val("1_5"), file(".report.json"), file(".versions"), file(".command.trace") into REPORT_retrieve_mapped_1_5
file ".versions"
file ".versions"

script:
"""
samtools view -buh -F 12 -o ${sample_id}_samtools.bam -@ $task.cpus ${bam}
rm ${bam}
samtools fastq -1 ${sample_id}_mapped_1.fq -2 ${sample_id}_mapped_2.fq ${sample_id}_samtools.bam
if [[ \$(cat ${is_pair}) == "True" ]];
then
samtools view -buh -F 12 -o ${sample_id}_samtools.bam -@ $task.cpus ${bam}
rm ${bam}
rm ${sample_id}_samtools.bam
samtools fastq -1 ${sample_id}_mapped_1.fq -2 ${sample_id}_mapped_2.fq ${sample_id}_samtools.bam
rm ${sample_id}_samtools.bam
renamePE_samtoolsFASTQ.py -1 ${sample_id}_mapped_1.fq -2 ${sample_id}_mapped_2.fq
else
samtools view -buh -F 4 -o ${sample_id}_samtools.bam -@ $task.cpus ${bam}
rm ${bam}
gzip *.headersRenamed_*.fq
samtools fastq ${sample_id}_samtools.bam > ${sample_id}_mapped.fq
rm ${sample_id}_samtools.bam
rm *.fq
fi
"""
}

process renamePE_1_4 {

tag { sample_id }
publishDir 'results/mapping/retrieve_mapped_{{ pid }}/'

if ( params.platformHTTP != null ) {
beforeScript "PATH=${workflow.projectDir}/bin:\$PATH; export PATH; set_dotfiles.sh; startup_POST.sh $params.projectId $params.pipelineId 1_5 $params.platformHTTP"
afterScript "final_POST.sh $params.projectId $params.pipelineId 1_5 $params.platformHTTP; report_POST.sh $params.projectId $params.pipelineId 1_5 $params.sampleName $params.reportHTTP $params.currentUserName $params.currentUserId retrieve_mapped_1_5 \"$params.platformSpecies\" true"
} else {
beforeScript "PATH=${workflow.projectDir}/bin:\$PATH; set_dotfiles.sh"
}

input:
set sample_id, file(fastq_pair) from OUT_retrieve_mapped_1_4

output:
set sample_id , file("*.headersRenamed*") into retrieve_mapped_out_1_4
set sample_id, val("1_5_retrieve_mapped"), file(".status"), file(".warning"), file(".fail"), file(".command.log") into STATUS_renamePE_1_5
set sample_id, val("retrieve_mapped_1_5"), val("1_5"), file(".report.json"), file(".versions"), file(".command.trace") into REPORT_renamePE_1_5
file ".versions"

script:
template "renamePE_samtoolsFASTQ.py"

}

IN_genome_size_1_6 = Channel.value(params.genomeSize)
.map{it -> it.toString().isNumber() ? it : exit (1, "The genomeSize parameter must be a number or a float. Provided value: '${params.genomeSize}'")}
Expand Down Expand Up @@ -1352,7 +1400,7 @@ process status {
publishDir "pipeline_status/$task_name"

input:
set sample_id, task_name, status, warning, fail, file(log) from STATUS_integrity_coverage_1_1.mix(STATUS_fastqc_1_2,STATUS_fastqc_report_1_2,STATUS_trimmomatic_1_2,STATUS_filter_poly_1_3,STATUS_bowtie_1_4,STATUS_report_bowtie_1_4,STATUS_retrieve_mapped_1_5,STATUS_check_coverage_1_6,STATUS_va_spades_1_7,STATUS_va_megahit_1_7,STATUS_report_viral_assembly_1_7,STATUS_assembly_mapping_1_8,STATUS_process_am_1_8,STATUS_pilon_1_9,STATUS_pilon_report_1_9,STATUS_split_assembly_1_10,STATUS_dengue_typing_assembly_1_11,STATUS_dengue_typing_reads_1_11,STATUS_mafft_1_12,STATUS_raxml_1_13,STATUS_report_raxml_1_13)
set sample_id, task_name, status, warning, fail, file(log) from STATUS_integrity_coverage_1_1.mix(STATUS_fastqc_1_2,STATUS_fastqc_report_1_2,STATUS_trimmomatic_1_2,STATUS_filter_poly_1_3,STATUS_bowtie_1_4,STATUS_report_bowtie_1_4,STATUS_retrieve_mapped_1_5,STATUS_renamePE_1_5,STATUS_check_coverage_1_6,STATUS_va_spades_1_7,STATUS_va_megahit_1_7,STATUS_report_viral_assembly_1_7,STATUS_assembly_mapping_1_8,STATUS_process_am_1_8,STATUS_pilon_1_9,STATUS_pilon_report_1_9,STATUS_split_assembly_1_10,STATUS_dengue_typing_assembly_1_11,STATUS_dengue_typing_reads_1_11,STATUS_mafft_1_12,STATUS_raxml_1_13,STATUS_report_raxml_1_13)

output:
file '*.status' into master_status
Expand Down Expand Up @@ -1421,7 +1469,7 @@ process report {
pid,
report_json,
version_json,
trace from REPORT_integrity_coverage_1_1.mix(REPORT_fastqc_1_2,REPORT_fastqc_report_1_2,REPORT_trimmomatic_1_2,REPORT_filter_poly_1_3,REPORT_bowtie_1_4,REPORT_report_bowtie_1_4,REPORT_retrieve_mapped_1_5,REPORT_check_coverage_1_6,REPORT_va_spades_1_7,REPORT_va_megahit_1_7,REPORT_report_viral_assembly_1_7,REPORT_assembly_mapping_1_8,REPORT_process_am_1_8,REPORT_pilon_1_9,REPORT_pilon_report_1_9,REPORT_split_assembly_1_10,REPORT_dengue_typing_assembly_1_11,REPORT_dengue_typing_reads_1_11,REPORT_mafft_1_12,REPORT_raxml_1_13,REPORT_report_raxml_1_13)
trace from REPORT_integrity_coverage_1_1.mix(REPORT_fastqc_1_2,REPORT_fastqc_report_1_2,REPORT_trimmomatic_1_2,REPORT_filter_poly_1_3,REPORT_bowtie_1_4,REPORT_report_bowtie_1_4,REPORT_retrieve_mapped_1_5,REPORT_renamePE_1_5,REPORT_check_coverage_1_6,REPORT_va_spades_1_7,REPORT_va_megahit_1_7,REPORT_report_viral_assembly_1_7,REPORT_assembly_mapping_1_8,REPORT_process_am_1_8,REPORT_pilon_1_9,REPORT_pilon_report_1_9,REPORT_split_assembly_1_10,REPORT_dengue_typing_assembly_1_11,REPORT_dengue_typing_reads_1_11,REPORT_mafft_1_12,REPORT_raxml_1_13,REPORT_report_raxml_1_13)

output:
file "*" optional true into master_report
Expand Down
140 changes: 0 additions & 140 deletions bin/renamePE_samtoolsFASTQ.py
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This file was deleted.

2 changes: 1 addition & 1 deletion templates/fastqc_report.py
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Original file line number Diff line number Diff line change
Expand Up @@ -165,7 +165,7 @@ def write_json_report(sample_id, data):
for cat, start_str in parser_map.items():

report_list = []
status_list= []
status_list = []

if cat == "per_base_sequence_content":
fs = 1
Expand Down
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