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add SIDLE workflow from d4straub/pipesidle
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,43 @@ | ||
| process SIDLE_ALIGN { | ||
| tag "$meta.region" | ||
| label 'process_medium' | ||
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| container 'docker.io/d4straub/pipesidle:0.1.0-beta' | ||
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| input: | ||
| tuple val(meta), path(kmers), path(seq) | ||
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| output: | ||
| tuple val(meta), path("*rep-seqs_align-map.qza"), emit: aligned_map | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.region}" | ||
| def primerfw = "${meta.fw_primer}" | ||
| def primerrv = "${meta.rv_primer}" | ||
| """ | ||
| # https://q2-sidle.readthedocs.io/en/latest/reconstruction.html#regional-alignment | ||
| export XDG_CONFIG_HOME="./xdgconfig" | ||
| export MPLCONFIGDIR="./mplconfigdir" | ||
| export NUMBA_CACHE_DIR="./numbacache" | ||
| qiime sidle align-regional-kmers \\ | ||
| --p-n-workers $task.cpus \\ | ||
| --i-kmers ${kmers} \\ | ||
| --i-rep-seq ${seq} \\ | ||
| --p-region ${meta.region} \\ | ||
| $args \\ | ||
| --o-regional-alignment ${prefix}_rep-seqs_align-map.qza | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| qiime2: \$( qiime --version | sed '1!d;s/.* //' ) | ||
| qiime2 plugin sidle: \$( qiime sidle --version | sed 's/ (.*//' | sed 's/.*version //' ) | ||
| q2-sidle: \$( qiime sidle --version | sed 's/.*version //' | sed 's/)//' ) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
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| process SIDLE_DBEXTRACT { | ||
| tag "$meta.region,$meta.region_length" | ||
| label 'process_medium' | ||
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| container 'docker.io/d4straub/pipesidle:0.1.0-beta' | ||
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| input: | ||
| tuple val(meta), path(table), path(seq), path(db_seq), path(db_tax) | ||
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| output: | ||
| tuple val(meta), path("db_*_kmers.qza"), emit: kmers | ||
| tuple val(meta), path("db_*_map.qza") , emit: map | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def prefix = task.ext.prefix ?: "${meta.region}" | ||
| def primerfw = "${meta.fw_primer}" | ||
| def primerrv = "${meta.rv_primer}" | ||
| def length = "${meta.region_length}" | ||
| """ | ||
| # https://q2-sidle.readthedocs.io/en/latest/database_preparation.html#prepare-a-regional-database-for-each-primer-set | ||
| export XDG_CONFIG_HOME="./xdgconfig" | ||
| export MPLCONFIGDIR="./mplconfigdir" | ||
| export NUMBA_CACHE_DIR="./numbacache" | ||
| #extract sequences | ||
| qiime feature-classifier extract-reads \\ | ||
| --p-n-jobs $task.cpus \\ | ||
| --i-sequences $db_seq \\ | ||
| $args \\ | ||
| --p-f-primer $primerfw \\ | ||
| --p-r-primer $primerrv \\ | ||
| --o-reads db_${prefix}.qza | ||
| #prepare to be used in alignment | ||
| qiime sidle prepare-extracted-region \\ | ||
| --p-n-workers $task.cpus \\ | ||
| --i-sequences db_${prefix}.qza \\ | ||
| --p-region "${prefix}" \\ | ||
| --p-fwd-primer $primerfw \\ | ||
| --p-rev-primer $primerrv \\ | ||
| --p-trim-length $length \\ | ||
| --o-collapsed-kmers db_${prefix}_${length}_kmers.qza \\ | ||
| --o-kmer-map db_${prefix}_${length}_map.qza | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| qiime2: \$( qiime --version | sed '1!d;s/.* //' ) | ||
| qiime2 plugin sidle: \$( qiime sidle --version | sed 's/ (.*//' | sed 's/.*version //' ) | ||
| q2-sidle: \$( qiime sidle --version | sed 's/.*version //' | sed 's/)//' ) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,50 @@ | ||
| process SIDLE_DBFILT { | ||
| label 'process_low' | ||
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| container 'docker.io/d4straub/pipesidle:0.1.0-beta' | ||
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| input: | ||
| path(seq) | ||
| path(tax) | ||
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| output: | ||
| path("db_filtered_sequences.qza") , emit: seq | ||
| path("db_filtered_sequences_tax.qza") , emit: tax | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def args2 = task.ext.args2 ?: '' | ||
| """ | ||
| # https://q2-sidle.readthedocs.io/en/latest/database_preparation.html#filtering-the-database | ||
| #pre-filtering should be very permissive! | ||
| export XDG_CONFIG_HOME="./xdgconfig" | ||
| export MPLCONFIGDIR="./mplconfigdir" | ||
| export NUMBA_CACHE_DIR="./numbacache" | ||
| # authors of SMURF recommend "--p-num-degenerates 3" for greengenes 13_8 database at 99% | ||
| # the RESCRIPt formatted Silva 128 database is filtered to exclude sequences with more than 5 degenerates [3], [4] | ||
| qiime rescript cull-seqs \\ | ||
| --p-n-jobs $task.cpus \\ | ||
| --i-sequences $seq \\ | ||
| $args \\ | ||
| --o-clean-sequences db_filtered_sequences.qza | ||
| #filtering a greengenes database for features missing a phylum (p__;) or kingdom(k__;) designation. | ||
| #CPU=1 | ||
| qiime taxa filter-seqs \\ | ||
| --i-sequences db_filtered_sequences.qza \\ | ||
| --i-taxonomy $tax \\ | ||
| $args2 \\ | ||
| --o-filtered-sequences db_filtered_sequences_tax.qza | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| qiime2: \$( qiime --version | sed '1!d;s/.* //' ) | ||
| qiime2 rescript: \$( qiime rescript --version | sed 's/ (.*//' | sed 's/.*version //' ) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,56 @@ | ||
| process SIDLE_DBRECON { | ||
| label 'process_medium' | ||
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| container 'docker.io/d4straub/pipesidle:0.1.0-beta' | ||
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| input: | ||
| val(metaid) | ||
| path(map) | ||
| path(aligned_map) | ||
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| output: | ||
| path("reconstruction_map.qza") , emit: reconstruction_map | ||
| path("reconstruction_summary.qza"), emit: reconstruction_summary | ||
| path("reconstruction_summary/*") , emit: visualisation | ||
| path "versions.yml" , emit: versions | ||
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| when: | ||
| task.ext.when == null || task.ext.when | ||
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| script: | ||
| def args = task.ext.args ?: '' | ||
| def db_input = "" | ||
| // sort the input so that the regions are sorted by sequence | ||
| def df = [metaid, map, aligned_map].transpose().sort{ it[0] } | ||
| for (i in df) { | ||
| db_input += " --p-region "+i[0]+" --i-kmer-map "+i[1]+" --i-regional-alignment "+i[2] | ||
| } | ||
| """ | ||
| #https://q2-sidle.readthedocs.io/en/latest/reconstruction.html#database-reconstruction | ||
| export XDG_CONFIG_HOME="./xdgconfig" | ||
| export MPLCONFIGDIR="./mplconfigdir" | ||
| export NUMBA_CACHE_DIR="./numbacache" | ||
| qiime sidle reconstruct-database \\ | ||
| --p-n-workers $task.cpus \\ | ||
| $db_input \\ | ||
| $args \\ | ||
| --o-database-map reconstruction_map.qza \\ | ||
| --o-database-summary reconstruction_summary.qza | ||
| #database summary can be used to evaluate the quality of the reconstruction; see Fuks, C; Elgart, M; Amir, A; et al (2018) “Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling.” Microbiome. 6:17. doi: 10.1186/s40168-017-0396-x | ||
| qiime metadata tabulate \\ | ||
| --m-input-file reconstruction_summary.qza \\ | ||
| --o-visualization reconstruction_summary.qzv | ||
| qiime tools export \\ | ||
| --input-path reconstruction_summary.qzv \\ | ||
| --output-path "reconstruction_summary" | ||
| cat <<-END_VERSIONS > versions.yml | ||
| "${task.process}": | ||
| qiime2: \$( qiime --version | sed '1!d;s/.* //' ) | ||
| qiime2 plugin sidle: \$( qiime sidle --version | sed 's/ (.*//' | sed 's/.*version //' ) | ||
| q2-sidle: \$( qiime sidle --version | sed 's/.*version //' | sed 's/)//' ) | ||
| END_VERSIONS | ||
| """ | ||
| } |
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