From 16d7fd347ddccd4943a0cdacb77c4c01e2bfc162 Mon Sep 17 00:00:00 2001 From: Robrecht Cannoodt Date: Wed, 31 Jan 2024 17:06:37 +0100 Subject: [PATCH 1/2] Fix argument issues in bgzip (#14) * fix argument issues * add reference for htslib to the bgzip component --- src/bgzip/config.vsh.yaml | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/bgzip/config.vsh.yaml b/src/bgzip/config.vsh.yaml index 159c33e8..c37db43c 100644 --- a/src/bgzip/config.vsh.yaml +++ b/src/bgzip/config.vsh.yaml @@ -6,6 +6,8 @@ functionality: documentation: https://www.htslib.org/doc/bgzip.html repository: https://github.com/samtools/htslib licence: MIT + reference: + doi: 10.1093/gigascience/giab007 requirements: commands: [ bgzip ] argument_groups: @@ -30,7 +32,7 @@ functionality: description: name of BGZF index file [file.gz.gzi] - name: Arguments arguments: - - name: offset + - name: --offset alternatives: -b type: integer description: decompress at virtual file pointer (0-based uncompressed offset) @@ -79,6 +81,7 @@ functionality: [[ "$par_binary" == "false" ]] && unset par_binary bgzip -c \ ${meta_cpus:+--threads "${meta_cpus}"} \ + ${par_offset:+-b "${par_offset}"} \ ${par_decompress:+-d} \ ${par_rebgzip:+-g} \ ${par_index:+-i} \ @@ -87,6 +90,7 @@ functionality: ${par_reindex:+-r} \ ${par_size:+-s "${par_size}"} \ ${par_test:+-t} \ + ${par_binary:+--binary} \ "$par_input" > "$par_output" test_resources: - type: bash_script From f54af0af84a78e0b2483cc708f514780f0c609a3 Mon Sep 17 00:00:00 2001 From: Kai Waldrant Date: Fri, 2 Feb 2024 10:02:03 +0100 Subject: [PATCH 2/2] Add pear (#10) * WIP * update arguments in config * add script code * Add test * update CHANGELOG * add requirements * Apply suggestions from code review Co-authored-by: Robrecht Cannoodt * Update with review comments * update test_data * update outputs * update with latest review * Apply suggestions from code review --------- Co-authored-by: Robrecht Cannoodt --- CHANGELOG.md | 7 +- src/pear/config.vsh.yaml | 159 +++++++++++++++++++++++++++++++++++ src/pear/help.txt | 91 ++++++++++++++++++++ src/pear/script.sh | 63 ++++++++++++++ src/pear/test.sh | 23 +++++ src/pear/test_data/a.1.fastq | 4 + src/pear/test_data/a.2.fastq | 4 + src/pear/test_data/script.sh | 10 +++ 8 files changed, 359 insertions(+), 2 deletions(-) create mode 100644 src/pear/config.vsh.yaml create mode 100644 src/pear/help.txt create mode 100644 src/pear/script.sh create mode 100644 src/pear/test.sh create mode 100644 src/pear/test_data/a.1.fastq create mode 100644 src/pear/test_data/a.2.fastq create mode 100755 src/pear/test_data/script.sh diff --git a/CHANGELOG.md b/CHANGELOG.md index 7af39f0b..276195c2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,13 +5,16 @@ ## NEW FEATURES * `arriba`: Detect gene fusions from RNA-seq data (PR #1). -* `busco`: Assess genome assembly and annotation completeness with single copy orthologs (PR #6). * `fastp`: An ultra-fast all-in-one FASTQ preprocessor (PR #3). +* `busco`: Assess genome assembly and annotation completeness with single copy orthologs (PR #6). + +* `featurecounts`: Assign sequence reads to genomic features (PR #11). + * `bgzip`: Add bgzip functionality to compress and decompress files (PR #13). -* `featurecounts`: Assign sequence reads to genomic features (PR #11). +* `pear`: Paired-end read merger (PR #10). ## MAJOR CHANGES diff --git a/src/pear/config.vsh.yaml b/src/pear/config.vsh.yaml new file mode 100644 index 00000000..6bd8fe3c --- /dev/null +++ b/src/pear/config.vsh.yaml @@ -0,0 +1,159 @@ +functionality: + name: pear + description: | + PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. + + PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer. + info: + keywords: [ "pair-end", "read", "merge" ] + homepage: https://cme.h-its.org/exelixis/web/software/pear + repository: https://github.com/tseemann/PEAR + documentation: https://cme.h-its.org/exelixis/web/software/pear/doc.html + reference: doi:10.1093/bioinformatics/btt593 + licence: "CC-BY-NC-SA-3.0" + requirements: + commands: [ pear , gzip ] + argument_groups: + - name: Inputs + arguments: + - name: --forward_fastq + alternatives: -f + type: file + description: Forward paired-end FASTQ file + required: true + example: "forward.fastq" + - name: --reverse_fastq + alternatives: -r + type: file + description: Reverse paired-end FASTQ file + required: true + example: "reverse.fastq" + - name: Outputs + arguments: + - name: --assembled + type: file + description: The output file containing assembled reads. Can be compressed with gzip. + required: true + direction: output + - name: --unassembled_forward + type: file + description: The output file containing forward reads that could not be assembled. Can be compressed with gzip. + required: true + direction: output + - name: --unassembled_reverse + type: file + description: The output file containing reverse reads that could not be assembled. Can be compressed with gzip. + required: true + direction: output + - name: --discarded + type: file + description: The output file containing reads that were discarded due to too low quality or too many uncalled bases. Can be compressed with gzip. + required: true + direction: output + - name: Arguments + arguments: + - name: --p_value + alternatives: -p + type: double + description: | + Specify a p-value for the statistical test. If the computed p-value of a possible assembly exceeds the specified p-value then paired-end read will not be assembled. Valid options are: 0.0001, 0.001, 0.01, 0.05 and 1.0. Setting 1.0 disables the test. + example: 0.01 + required: false + - name: --min_overlap + alternatives: -v + type: integer + description: | + Specify the minimum overlap size. The minimum overlap may be set to 1 when the statistical test is used. However, further restricting the minimum overlap size to a proper value may reduce false-positive assembles. + required: false + example: 10 + - name: --max_assembly_length + alternatives: -m + type: integer + description: | + Specify the maximum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled sequences may be arbitrary long. + required: false + example: 0 + - name: --min_assembly_length + alternatives: -n + type: integer + description: | + Specify the minimum possible length of the assembled sequences. Setting this value to 0 disables the restriction and assembled sequences may be arbitrary short. + required: false + example: 0 + - name: --min_trim_length + alternatives: -t + type: integer + description: | + Specify the minimum length of reads after trimming the low quality part (see option -q) + required: false + example: 1 + - name: --quality_threshold + alternatives: -q + type: integer + description: | + Specify the quality threshold for trimming the low quality part of a read. If the quality scores of two consecutive bases are strictly less than the specified threshold, the rest of the read will be trimmed. + required: false + example: 0 + - name: --max_uncalled_base + alternatives: -u + type: double + description: | + Specify the maximal proportion of uncalled bases in a read. Setting this value to 0 will cause PEAR to discard all reads containing uncalled bases. The other extreme setting is 1 which causes PEAR to process all reads independent on the number of uncalled bases. + example: 1.0 + required: false + - name: --test_method + alternatives: -g + type: integer + description: | + Specify the type of statistical test. Two options are available. 1: Given the minimum allowed overlap, test using the highest OES. Note that due to its discrete nature, this test usually yields a lower p-value for the assembled read than the cut- off (specified by -p). For example, setting the cut-off to 0.05 using this test, the assembled reads might have an actual p-value of 0.02. + 2. Use the acceptance probability (m.a.p). This test methods computes the same probability as test method 1. However, it assumes that the minimal overlap is the observed overlap with the highest OES, instead of the one specified by -v. Therefore, this is not a valid statistical test and the 'p-value' is in fact the maximal probability for accepting the assembly. Nevertheless, we observed in practice that for the case the actual overlap sizes are relatively small, test 2 can correctly assemble more reads with only slightly higher false-positive rate. + required: false + example: 1 + - name: --emperical_freqs + alternatives: -e + type: boolean_true + description: | + Disable empirical base frequencies. + - name: --score_method + alternatives: -s + type: integer + description: | + Specify the scoring method. 1. OES with +1 for match and -1 for mismatch. 2: Assembly score (AS). Use +1 for match and -1 for mismatch multiplied by base quality scores. 3: Ignore quality scores and use +1 for a match and -1 for a mismatch. + required: false + example: 2 + - name: --phred_base + alternatives: -b + type: integer + description: | + Base PHRED quality score. + required: false + example: 33 + - name: --cap + alternatives: -c + type: integer + description: | + Specify the upper bound for the resulting quality score. If set to zero, capping is disabled. + required: false + example: 40 + - name: --nbase + alternatives: -z + type: boolean_true + description: | + When merging a base-pair that consists of two non-equal bases out of which none is degenerate, set the merged base to N and use the highest quality score of the two bases + resources: + - type: bash_script + path: script.sh + test_resources: + - type: bash_script + path: test.sh + - type: file + path: test_data +platforms: + - type: docker + image: quay.io/biocontainers/pear:0.9.6--h9d449c0_10 + setup: + - type: docker + run: | + version=$(pear -h | grep 'PEAR v' | sed 's/PEAR v//' | sed 's/ .*//') && \ + echo "pear: $version" > /var/software_versions.txt + - type: nextflow \ No newline at end of file diff --git a/src/pear/help.txt b/src/pear/help.txt new file mode 100644 index 00000000..d8e42285 --- /dev/null +++ b/src/pear/help.txt @@ -0,0 +1,91 @@ +```bash +pear -h +``` + + ____ _____ _ ____ +| _ \| ____| / \ | _ \ +| |_) | _| / _ \ | |_) | +| __/| |___ / ___ \| _ < +|_| |_____/_/ \_\_| \_\ +PEAR v0.9.6 [January 15, 2015] - [+bzlib +zlib] + +Citation - PEAR: a fast and accurate Illumina Paired-End reAd mergeR +Zhang et al (2014) Bioinformatics 30(5): 614-620 | doi:10.1093/bioinformatics/btt593 + +License: Creative Commons Licence +Bug-reports and requests to: Tomas.Flouri@h-its.org and Jiajie.Zhang@h-its.org + + +Usage: pear +Standard (mandatory): + -f, --forward-fastq Forward paired-end FASTQ file. + -r, --reverse-fastq Reverse paired-end FASTQ file. + -o, --output Output filename. +Optional: + -p, --p-value Specify a p-value for the statistical test. If the computed + p-value of a possible assembly exceeds the specified p-value + then paired-end read will not be assembled. Valid options + are: 0.0001, 0.001, 0.01, 0.05 and 1.0. Setting 1.0 disables + the test. (default: 0.01) + -v, --min-overlap Specify the minimum overlap size. The minimum overlap may be + set to 1 when the statistical test is used. However, further + restricting the minimum overlap size to a proper value may + reduce false-positive assembles. (default: 10) + -m, --max-assembly-length Specify the maximum possible length of the assembled + sequences. Setting this value to 0 disables the restriction + and assembled sequences may be arbitrary long. (default: 0) + -n, --min-assembly-length Specify the minimum possible length of the assembled + sequences. Setting this value to 0 disables the restriction + and assembled sequences may be arbitrary short. (default: + 50) + -t, --min-trim-length Specify the minimum length of reads after trimming the low + quality part (see option -q). (default: 1) + -q, --quality-threshold Specify the quality score threshold for trimming the low + quality part of a read. If the quality scores of two + consecutive bases are strictly less than the specified + threshold, the rest of the read will be trimmed. (default: + 0) + -u, --max-uncalled-base Specify the maximal proportion of uncalled bases in a read. + Setting this value to 0 will cause PEAR to discard all reads + containing uncalled bases. The other extreme setting is 1 + which causes PEAR to process all reads independent on the + number of uncalled bases. (default: 1) + -g, --test-method Specify the type of statistical test. Two options are + available. (default: 1) + 1: Given the minimum allowed overlap, test using the highest + OES. Note that due to its discrete nature, this test usually + yields a lower p-value for the assembled read than the cut- + off (specified by -p). For example, setting the cut-off to + 0.05 using this test, the assembled reads might have an + actual p-value of 0.02. + + 2. Use the acceptance probability (m.a.p). This test methods + computes the same probability as test method 1. However, it + assumes that the minimal overlap is the observed overlap + with the highest OES, instead of the one specified by -v. + Therefore, this is not a valid statistical test and the + 'p-value' is in fact the maximal probability for accepting + the assembly. Nevertheless, we observed in practice that for + the case the actual overlap sizes are relatively small, test + 2 can correctly assemble more reads with only slightly + higher false-positive rate. + -e, --empirical-freqs Disable empirical base frequencies. (default: use empirical + base frequencies) + -s, --score-method Specify the scoring method. (default: 2) + 1. OES with +1 for match and -1 for mismatch. + 2: Assembly score (AS). Use +1 for match and -1 for mismatch + multiplied by base quality scores. + 3: Ignore quality scores and use +1 for a match and -1 for a + mismatch. + -b, --phred-base Base PHRED quality score. (default: 33) + -y, --memory Specify the amount of memory to be used. The number may be + followed by one of the letters K, M, or G denoting + Kilobytes, Megabytes and Gigabytes, respectively. Bytes are + assumed in case no letter is specified. + -c, --cap Specify the upper bound for the resulting quality score. If + set to zero, capping is disabled. (default: 40) + -j, --threads Number of threads to use + -z, --nbase When merging a base-pair that consists of two non-equal + bases out of which none is degenerate, set the merged base + to N and use the highest quality score of the two bases + -h, --help This help screen. \ No newline at end of file diff --git a/src/pear/script.sh b/src/pear/script.sh new file mode 100644 index 00000000..f7d6a28f --- /dev/null +++ b/src/pear/script.sh @@ -0,0 +1,63 @@ +#!/bin/bash + +## VIASH START +## VIASH END + +[[ "$par_emperical_freqs" == "false" ]] && unset par_emperical_freqs +[[ "$par_nbase" == "false" ]] && unset par_nbase + +if [[ "${par_forward_fastq##*.}" == "gz" ]]; then + gunzip $par_forward_fastq + par_forward_fastq=${par_forward_fastq%.*} +fi +if [[ "${par_reverse_fastq##*.}" == "gz" ]]; then + gunzip $par_reverse_fastq + par_reverse_fastq=${par_reverse_fastq%.*} +fi + +output_dir=$(mktemp -d -p "$meta_temp_dir" "pear.XXXXXX") + +pear \ + -f "$par_forward_fastq" \ + -r "$par_reverse_fastq" \ + -o "$output_dir" \ + ${par_p_value:+-p "${par_p_value}"} \ + ${par_min_overlap:+-v "${par_min_overlap}"} \ + ${par_max_assembly_length:+-m "${par_max_assembly_length}"} \ + ${par_min_assembly_length:+-n "${par_min_assembly_length}"} \ + ${par_min_trim_length:+-t "${par_min_trim_length}"} \ + ${par_quality_threshold:+-q "${par_quality_threshold}"} \ + ${par_max_uncalled_base:+-u "${par_max_uncalled_base}"} \ + ${par_test_method:+-g "${par_test_method}"} \ + ${par_score_method:+-s "${par_score_method}"} \ + ${par_phred_base:+-b "${par_phred_base}"} \ + ${meta_memory_mb:+--memory "${meta_memory_mb}M"} \ + ${par_cap:+-c "${par_cap}"} \ + ${meta_cpus:+-j "${meta_cpus}"} \ + ${par_emperical_freqs:+-e} \ + ${par_nbase:+-z} + + +if [[ "${par_assembled##*.}" == "gz" ]]; then + gzip -9 -c ${output_dir}.assembled.fastq > ${par_assembled} +else + mv ${output_dir}.assembled.fastq ${par_assembled} +fi + +if [[ "${par_unassembled_forward##*.}" == "gz" ]]; then + gzip -9 -c ${output_dir}.unassembled.forward.fastq > ${par_unassembled_forward} +else + mv ${output_dir}.unassembled.forward.fastq ${par_unassembled_forward} +fi + +if [[ "${par_unassembled_reverse##*.}" == "gz" ]]; then + gzip -9 -c ${output_dir}.unassembled.reverse.fastq > ${par_unassembled_reverse} +else + mv ${output_dir}.unassembled.reverse.fastq ${par_unassembled_reverse} +fi + +if [[ "${par_discarded##*.}" == "gz" ]]; then + gzip -9 -c ${output_dir}.discarded.fastq > ${par_discarded} +else + mv ${output_dir}.discarded.fastq ${par_discarded} +fi diff --git a/src/pear/test.sh b/src/pear/test.sh new file mode 100644 index 00000000..67870bf4 --- /dev/null +++ b/src/pear/test.sh @@ -0,0 +1,23 @@ +#!/bin/bash + +set -e + +dir_in="${meta_resources_dir%/}/test_data" + +echo "> Run PEAR" +"$meta_executable" \ + --forward_fastq "$dir_in/a.1.fastq" \ + --reverse_fastq "$dir_in/a.2.fastq" \ + --assembled "test.assembled.fastq.gz" \ + --unassembled_forward "test.unassembled.forward.fastq.gz" \ + --unassembled_reverse "test.unassembled.reverse.fastq.gz" \ + --discarded "test.discarded.fastq.gz" \ + --p_value 0.01 + +echo ">> Checking output" +[ ! -f "test.assembled.fastq.gz" ] && echo "Output file test.assembled.fastq.gz does not exist" && exit 1 +[ ! -f "test.unassembled.forward.fastq.gz" ] && echo "Output file test.unassembled.forward.fastq.gz does not exist" && exit 1 +[ ! -f "test.unassembled.reverse.fastq.gz" ] && echo "Output file test.unassembled.reverse.fastq.gz does not exist" && exit 1 +[ ! -f "test.discarded.fastq.gz" ] && echo "Output file ftest.discarded.fastq.gz does not exist" && exit 1 + +echo "> Test successful" \ No newline at end of file diff --git a/src/pear/test_data/a.1.fastq b/src/pear/test_data/a.1.fastq new file mode 100644 index 00000000..42735560 --- /dev/null +++ b/src/pear/test_data/a.1.fastq @@ -0,0 +1,4 @@ +@1 +ACGGCAT ++ +!!!!!!! diff --git a/src/pear/test_data/a.2.fastq b/src/pear/test_data/a.2.fastq new file mode 100644 index 00000000..42735560 --- /dev/null +++ b/src/pear/test_data/a.2.fastq @@ -0,0 +1,4 @@ +@1 +ACGGCAT ++ +!!!!!!! diff --git a/src/pear/test_data/script.sh b/src/pear/test_data/script.sh new file mode 100755 index 00000000..016910a8 --- /dev/null +++ b/src/pear/test_data/script.sh @@ -0,0 +1,10 @@ +# pear test data + +# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/fastp/test + +if [ ! -d /tmp/snakemake-wrappers ]; then + git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers +fi + +cp -r /tmp/snakemake-wrappers/bio/fastp/test/reads/pe/* src/pear/test_data +