Commit c033932f authored by Damien VINTACHE's avatar Damien VINTACHE

change TZ definition

parent 9985aec3
# coding: utf-8
import datetime
import logging
import os
......@@ -695,7 +696,7 @@ if "denoiser" in config["global"]:
params: options = getOptions("import")
singularity: "docker://qiime2/core:latest"
shell: """
TZ=‘Europe/Paris’ qiime tools import --input-path {input} --output-path {output} {params.options}
TZ="Europe/Paris" qiime tools import --input-path {input} --output-path {output} {params.options}
"""
#####################
......@@ -784,7 +785,7 @@ if "denoiser" in config["global"]:
# conda: qiime2_yml
singularity: "docker://qiime2/core:latest"
shell: """
export TZ=‘Europe/Paris’
export TZ="Europe/Paris"
qiime dada2 {params.lib_type} --i-demultiplexed-seqs {input} {params.options} --o-table {output[0]} --o-representative-sequences {output[1]} --o-denoising-stats {output[2]}
qiime metadata tabulate --m-input-file {output[2]} --o-visualization {output[3]}
qiime tools export --input-path {output[3]} --output-path {output[4]}
......@@ -823,7 +824,7 @@ if "denoiser" in config["global"]:
# conda: qiime2_yml
singularity: "docker://qiime2/core:latest"
shell: """
export TZ=‘Europe/Paris’
export TZ="Europe/Paris"
qiime feature-table summarize --i-table {input[0]} --o-visualization {output[0]}
qiime feature-table tabulate-seqs --i-data {input[1]} --o-visualization {output[1]}
qiime tools export --input-path {output[0]} --output-path `dirname $(dirname {output[1]})`/table_html
......@@ -935,7 +936,7 @@ if "denoiser" in config["global"]:
# conda: qiime2_yml
singularity: "docker://qiime2/core:latest"
shell: """
export TZ=‘Europe/Paris’
export TZ="Europe/Paris"
qiime phylogeny align-to-tree-mafft-fasttree --i-sequences {input} --o-alignment {output[0]} --o-masked-alignment {output[1]} --o-tree {output[2]} --o-rooted-tree {output[3]} {params.options}
qiime tools export --input-path {output[3]} --output-path `dirname $(dirname {output[3]})`
"""
......@@ -973,7 +974,7 @@ if "denoiser" in config["global"]:
# conda: qiime2_yml
singularity: "docker://qiime2/core:latest"
shell: """
export TZ=‘Europe/Paris’
export TZ="Europe/Paris"
qiime diversity core-metrics-phylogenetic --i-phylogeny {input[0]} --i-table {input[1]} --m-metadata-file {input[2]} --o-rarefied-table {output[0]} --o-faith-pd-vector {output[1]} --o-observed-otus-vector {output[2]} --o-shannon-vector {output[3]} --o-evenness-vector {output[4]} --o-unweighted-unifrac-distance-matrix {output[5]} --o-weighted-unifrac-distance-matrix {output[6]} --o-jaccard-distance-matrix {output[7]} --o-bray-curtis-distance-matrix {output[8]} --o-unweighted-unifrac-pcoa-results {output[9]} --o-weighted-unifrac-pcoa-results {output[10]} --o-jaccard-pcoa-results {output[11]} --o-bray-curtis-pcoa-results {output[12]} --o-unweighted-unifrac-emperor {output[13]} --o-weighted-unifrac-emperor {output[14]} --o-jaccard-emperor {output[15]} --o-bray-curtis-emperor {output[16]} {params.options}
qiime tools export --input-path {output[16]} --output-path {output.braycurtis}
qiime tools export --input-path {output[15]} --output-path {output.jaccard}
......@@ -993,7 +994,7 @@ if "denoiser" in config["global"]:
# conda: qiime2_yml
singularity: "docker://qiime2/core:latest"
shell: """
export TZ=‘Europe/Paris’
export TZ="Europe/Paris"
qiime diversity alpha-group-significance --i-alpha-diversity {input[0]} --m-metadata-file {input[2]} --o-visualization {output[2]}
qiime diversity alpha-group-significance --i-alpha-diversity {input[1]} --m-metadata-file {input[2]} --o-visualization {output[3]}
qiime tools export --input-path {output[2]} --output-path `dirname {output[0]}`
......@@ -1014,7 +1015,7 @@ if "denoiser" in config["global"]:
# conda: qiime2_yml
singularity: "docker://qiime2/core:latest"
shell: """
export TZ=‘Europe/Paris’
export TZ="Europe/Paris"
qiime diversity alpha-rarefaction --i-table {input[0]} --i-phylogeny {input[1]} --m-metadata-file {input[2]} --o-visualization {output[0]} {params.options}
qiime tools export --input-path {output[0]} --output-path `dirname {output[1]}`
"""
......
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