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Updates and fixes - se/pe
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@tverbeiren
tverbeiren committed Feb 7, 2024
1 parent f67eeac commit b93f95c
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Showing 2 changed files with 43 additions and 112 deletions.
11 changes: 8 additions & 3 deletions src/cutadapt/config.vsh.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -164,7 +164,6 @@ functionality:
description: |
Which of the reads in a paired-end read have to match the
filtering criterion in order for the pair to be filtered.
default: any
- name: --interleaved
type: boolean_true
description: |
Expand All @@ -173,6 +172,12 @@ functionality:
####################################################################
- name: Input parameters
arguments:
- name: --input
type: file
multiple: true
required: true
description: |
Input fastq files. Paired reads are delimited with a space.
- name: --error_rate
alternatives: [-E, --errors]
type: double
Expand Down Expand Up @@ -329,7 +334,7 @@ functionality:
- name: Filtering of processed reads
description: |
Filters are applied after above read modifications. Paired-end reads are
always discarded pairwise (see also --pair-filter).
always discarded pairwise (see also --pair_filter).
arguments:
- name: --minimum_length
alternatives: [-m]
Expand Down Expand Up @@ -397,7 +402,7 @@ functionality:
Write trimmed reads to this directory and name the files using {name}.
FASTQ or FASTA format is chosen depending on input.
Summary report is sent to standard output.
default: output/
default: output
direction: output
required: true
must_exist: true
Expand Down
144 changes: 35 additions & 109 deletions src/cutadapt/script.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -6,101 +6,20 @@ else
mkdir -p "$par_output"
fi

echo "par_pair_adapters: $par_pair_adapters"
echo "par_pair_filter: $par_pair_filter"
echo "par_interleaved: $par_interleaved"
echo "par_error_rate: $par_error_rate"
echo "par_no_indels: $par_no_indels"
echo "par_times: $par_times"
echo "par_overlap: $par_overlap"
echo "par_match_read_wildcards: $par_match_read_wildcards"
echo "no_match_adapter_wildcards: $no_match_adapter_wildcards"
echo "par_action: $par_action"
echo "par_revcomp: $par_revcomp"
echo "par_cut: $par_cut"
echo "par_cutR2: $par_cutR2"
echo "par_nextseq_trim: $par_nextseq_trim"
echo "par_quality_cutoff: $par_quality_cutoff"
echo "par_quality_cutoffR2: $par_quality_cutoffR2"
echo "par_quality_base: $par_quality_base"
echo "par_poly_a: $par_poly_a"
echo "par_length: $par_length"
echo "par_trim_n: $par_trim_n"
echo "par_length_tag: $par_length_tag"
echo "par_strip_suffix: $par_strip_suffix"
echo "par_prefix: $par_prefix"
echo "par_suffix: $par_suffix"
echo "par_rename: $par_rename"
echo "par_zero_cap: $par_zero_cap"
echo "par_minimum_length: $par_minimum_length"
echo "par_maximum_length: $par_maximum_length"
echo "par_max_n: $par_max_n"
echo "par_max_expected_errors: $par_max_expected_errors"
echo "par_max_average_error_rate: $par_max_average_error_rate"
echo "par_discard_trimmed: $par_discard_trimmed"
echo "par_discard_untrimmed: $par_discard_untrimmed"
echo "par_discard_casava: $par_discard_casava"
echo "par_report: $par_report"
echo "par_json: $par_json"
echo "par_output: $par_output"
echo "par_fasta: $par_fasta"
echo "par_info_file: $par_info_file"

# Do we get explicit adapter sequences or a FASTA file?
# Let the underlying tool deal with inconsistant states.
adapter_mode_R1=""
if [ ! -z "${par_adapter_fasta+set}" ]; then
adapter_mode_R1="fasta"
else
adapter_mode_R1="plain"
fi

front_mode_R1=""
if [ ! -z "${par_front_fasta+set}" ]; then
front_mode_R1="fasta"
else
front_mode_R1="plain"
fi

anywhere_mode_R1=""
if [ ! -z "${par_anywhere_fasta+set}" ]; then
anywhere_mode_R1="fasta"
else
anywhere_mode_R1="plain"
fi

adapter_mode_R2=""
if [ ! -z "${par_adapter_fastaR2+set}" ]; then
adapter_mode_R2="fasta"
else
adapter_mode_R2="plain"
fi

front_mode_R2=""
if [ ! -z "${par_front_fastaR2+set}" ]; then
front_mode_R2="fasta"
else
front_mode_R2="plain"
fi

anywhere_mode_R2=""
if [ ! -z "${par_anywhere_fastaR2+set}" ]; then
anywhere_mode_R2="fasta"
else
anywhere_mode_R2="plain"
fi

# Init
###########################################################
echo "Running cutadapt"
echo
echo "Adapter settings"
echo "----------------"
echo "Adapter Mode R1 : $adapter_mode_R1"
echo "Front Mode R1 : $front_mode_R1"
echo "Anywhere Mode R1 : $anywhere_mode_R1"
echo "Adapter Mode R2 : $adapter_mode_R2"
echo "Front Mode R2 : $front_mode_R2"
echo "Anywhere Mode R2 : $anywhere_mode_R2"
echo
echo ">> Paired-end data or not?"
IFS=':' read -a inputs <<< "$par_input"
input=$(echo $par_input | tr ':' ' ')

nr_inputs="${#inputs[@]}"

[[ $nr_inputs = 1 ]] && echo " Single end" && mode="se"
[[ $nr_inputs = 2 ]] && echo " Paired end" && mode="pe"
[[ $nr_inputs = 3 ]] && echo " Too much input !!!" && exit 1

# Adapter arguments
# - paired and single-end
Expand Down Expand Up @@ -134,8 +53,7 @@ echo ">> Parsing arguments for paired-end reads"
paired_args=$(echo \
${par_pair_adapters:+--pair-adapters} \
${par_pair_filter:+--pair-filter "${par_pair_filter}"} \
${par_interleaved:+--interleaved} \
${par_interleaved:+--interleaved}
)
echo "Arguments to cutadapt:"
echo $paired_args
Expand All @@ -150,7 +68,7 @@ echo ">> Parsing input arguments"
[[ "$par_revcomp" == "false" ]] && unset par_revcomp

input_args=$(echo \
${par_error_rate:+-error-rate "${par_error_rate}"} \
${par_error_rate:+--error-rate "${par_error_rate}"} \
${par_no_indels:+--no-indels} \
${par_times:+--times "${par_times}"} \
${par_overlap:+--overlap "${par_overlap}"} \
Expand Down Expand Up @@ -221,23 +139,31 @@ echo ">> Output arguments"
[[ "$par_fasta" == "false" ]] && unset par_fasta
[[ "$par_info_file" == "false" ]] && unset par_info_file

# -o "$par_outputDir/{name}_R1_001.fastq" \
# -p "$par_outputDir/{name}_R2_001.fastq" \

output_args=$(echo \
${par_report:+--report "${par_report}"} \
${par_json:+--json} \
-o "$par_output/{name}_R1_001.fastq" \
-p "$par_output/{name}_R1_001.fastq" \
${par_fasta:+--fasta} \
${par_info_file:+--info-file} \
)
if [ $mode = "se" ]; then
output_args=$(echo \
${par_report:+--report "${par_report}"} \
${par_json:+--json} \
--output "$par_output/{name}_R1_001.fastq" \
${par_fasta:+--fasta} \
${par_info_file:+--info-file} \
)
else
output_args=$(echo \
${par_report:+--report "${par_report}"} \
${par_json:+--json} \
--output "$par_output/{name}_R1_001.fastq" \
--paired-output "$par_output/{name}_R2_001.fastq" \
${par_fasta:+--fasta} \
${par_info_file:+--info-file} \
)
fi
echo "Arguments to cutadapt:"
echo $output_args
echo

echo ">> Full CLI to be run:"
cli=$(echo "cutadapt" \
cli=$(echo \
$input \
$adapter_args \
$paired_args \
$input_args \
Expand All @@ -246,6 +172,6 @@ cli=$(echo "cutadapt" \
$output_args
)

echo $cli
echo cutadapt $cli | sed -e 's/--/\r\n --/g'

# $( "$cli" ) > $par_output/report.txt
cutadapt $cli | tee $par_output/report.txt

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