From 4d334b97068d51ec1e1a7040579d3901ea7cf5c9 Mon Sep 17 00:00:00 2001 From: daniel Date: Fri, 3 Nov 2023 09:15:57 +0100 Subject: [PATCH 1/5] export MPLCONFIGDIR --- modules/local/qiime2_alphararefaction.nf | 1 + modules/local/qiime2_ancom_asv.nf | 1 + modules/local/qiime2_ancom_tax.nf | 1 + modules/local/qiime2_barplot.nf | 1 + modules/local/qiime2_classify.nf | 1 + modules/local/qiime2_diversity_adonis.nf | 1 + modules/local/qiime2_diversity_alpha.nf | 1 + modules/local/qiime2_diversity_beta.nf | 1 + modules/local/qiime2_diversity_betaord.nf | 1 + modules/local/qiime2_diversity_core.nf | 1 + modules/local/qiime2_export_absolute.nf | 1 + modules/local/qiime2_export_relasv.nf | 1 + modules/local/qiime2_export_reltax.nf | 1 + modules/local/qiime2_extract.nf | 1 + modules/local/qiime2_featuretable_group.nf | 1 + modules/local/qiime2_filtersamples.nf | 1 + modules/local/qiime2_filtertaxa.nf | 1 + modules/local/qiime2_inasv.nf | 2 ++ modules/local/qiime2_inseq.nf | 2 ++ modules/local/qiime2_intax.nf | 2 ++ modules/local/qiime2_intree.nf | 2 ++ modules/local/qiime2_train.nf | 1 + modules/local/qiime2_tree.nf | 1 + 23 files changed, 27 insertions(+) diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index 273749ba..e4cb923f 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -24,6 +24,7 @@ process QIIME2_ALPHARAREFACTION { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" maxdepth=\$(count_table_minmax_reads.py $stats maximum 2>&1) diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index 52c599c4..ce580997 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -25,6 +25,7 @@ process QIIME2_ANCOM_ASV { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime composition add-pseudocount \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index 3c065bb3..e5033d25 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -23,6 +23,7 @@ process QIIME2_ANCOM_TAX { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" mkdir ancom # Sum data at the specified level diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index a06100d4..73b6b13b 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -26,6 +26,7 @@ process QIIME2_BARPLOT { def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": "" """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime taxa barplot \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index 96910c9a..e21c082c 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -24,6 +24,7 @@ process QIIME2_CLASSIFY { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime feature-classifier classify-sklearn \\ --i-classifier ${trained_classifier} \\ diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 6b81f00e..967685b2 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -23,6 +23,7 @@ process QIIME2_DIVERSITY_ADONIS { def args = task.ext.args ?: '' """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime diversity adonis \\ --p-n-jobs $task.cpus \\ diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index baebc03e..efe1d669 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -22,6 +22,7 @@ process QIIME2_DIVERSITY_ALPHA { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime diversity alpha-group-significance \\ --i-alpha-diversity ${core} \\ diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 44df25f9..044acaa5 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -22,6 +22,7 @@ process QIIME2_DIVERSITY_BETA { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime diversity beta-group-significance \\ --i-distance-matrix ${core} \\ diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index b29bd99e..ad7537b8 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -22,6 +22,7 @@ process QIIME2_DIVERSITY_BETAORD { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" mkdir beta_diversity qiime emperor plot \\ diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index 22235dfb..d248ae1a 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -32,6 +32,7 @@ process QIIME2_DIVERSITY_CORE { export UNIFRAC_USE_GPU=N export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1) if [ \"\$mindepth\" -lt \"$mindepth\" ]; then mindepth=$mindepth; fi diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index 57c03a5e..9f70976b 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -30,6 +30,7 @@ process QIIME2_EXPORT_ABSOLUTE { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" #produce raw count table in biom format "table/feature-table.biom" qiime tools export \\ diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index 58e05b58..a8856728 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -21,6 +21,7 @@ process QIIME2_EXPORT_RELASV { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" #convert to relative abundances qiime feature-table relative-frequency \\ diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index c5b93d7c..50de8e5e 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -24,6 +24,7 @@ process QIIME2_EXPORT_RELTAX { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" ##on several taxa level array=(\$(seq ${tax_agglom_min} 1 ${tax_agglom_max})) diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index 6889befb..37c99989 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -23,6 +23,7 @@ process QIIME2_EXTRACT { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" ### Import qiime tools import \\ diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index d47ee14f..b6826132 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -22,6 +22,7 @@ process QIIME2_FEATURETABLE_GROUP { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime feature-table filter-samples \\ --i-table "${table}" \\ diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index 7f64e7e2..5bb4a2cf 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -24,6 +24,7 @@ process QIIME2_FILTERSAMPLES { def prefix = task.ext.prefix ?: "${filter}" """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime feature-table filter-samples \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index 39cbb82c..0590f3fd 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -29,6 +29,7 @@ process QIIME2_FILTERTAXA { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" if ! [ \"${exclude_taxa}\" = \"none\" ]; then #filter sequences diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf index d4848ba7..20fb526e 100644 --- a/modules/local/qiime2_inasv.nf +++ b/modules/local/qiime2_inasv.nf @@ -21,6 +21,8 @@ process QIIME2_INASV { script: """ + export MPLCONFIGDIR="\${PWD}/HOME" + # remove first line if needed sed '/^# Constructed from biom file/d' "$asv" > biom-table.txt diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf index 7c7c2007..7c966a61 100644 --- a/modules/local/qiime2_inseq.nf +++ b/modules/local/qiime2_inseq.nf @@ -21,6 +21,8 @@ process QIIME2_INSEQ { script: """ + export MPLCONFIGDIR="\${PWD}/HOME" + qiime tools import \\ --input-path "$seq" \\ --type 'FeatureData[Sequence]' \\ diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf index b9c3b039..6a208974 100644 --- a/modules/local/qiime2_intax.nf +++ b/modules/local/qiime2_intax.nf @@ -23,6 +23,8 @@ process QIIME2_INTAX { script: def script_cmd = script ? "$script $tax" : "cp $tax tax.tsv" """ + export MPLCONFIGDIR="\${PWD}/HOME" + $script_cmd qiime tools import \\ diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf index a7a3ff3b..ec4e85d1 100644 --- a/modules/local/qiime2_intree.nf +++ b/modules/local/qiime2_intree.nf @@ -21,6 +21,8 @@ process QIIME2_INTREE { script: """ + export MPLCONFIGDIR="\${PWD}/HOME" + qiime tools import \\ --type 'Phylogeny[Rooted]' \\ --input-path $tree \\ diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 4c4d69b2..892d510a 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -23,6 +23,7 @@ process QIIME2_TRAIN { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" #Train classifier qiime feature-classifier fit-classifier-naive-bayes \\ diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index 6e7a89fe..99ef87b4 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -22,6 +22,7 @@ process QIIME2_TREE { script: """ export XDG_CONFIG_HOME="\${PWD}/HOME" + export MPLCONFIGDIR="\${PWD}/HOME" qiime alignment mafft \\ --i-sequences ${repseq} \\ From 8496c55948e7363504eb610ca34620a39d11bf4f Mon Sep 17 00:00:00 2001 From: daniel Date: Fri, 3 Nov 2023 15:05:00 +0100 Subject: [PATCH 2/5] change to tmp and export NUMBA_CACHE_DIR --- modules/local/qiime2_alphararefaction.nf | 5 +++-- modules/local/qiime2_ancom_asv.nf | 5 +++-- modules/local/qiime2_ancom_tax.nf | 5 +++-- modules/local/qiime2_barplot.nf | 5 +++-- modules/local/qiime2_classify.nf | 5 +++-- modules/local/qiime2_diversity_adonis.nf | 5 +++-- modules/local/qiime2_diversity_alpha.nf | 5 +++-- modules/local/qiime2_diversity_beta.nf | 5 +++-- modules/local/qiime2_diversity_betaord.nf | 5 +++-- modules/local/qiime2_diversity_core.nf | 5 +++-- modules/local/qiime2_export_absolute.nf | 5 +++-- modules/local/qiime2_export_relasv.nf | 5 +++-- modules/local/qiime2_export_reltax.nf | 5 +++-- modules/local/qiime2_extract.nf | 5 +++-- modules/local/qiime2_featuretable_group.nf | 5 +++-- modules/local/qiime2_filtersamples.nf | 5 +++-- modules/local/qiime2_filtertaxa.nf | 5 +++-- modules/local/qiime2_inasv.nf | 3 ++- modules/local/qiime2_inseq.nf | 3 ++- modules/local/qiime2_intax.nf | 3 ++- modules/local/qiime2_intree.nf | 3 ++- modules/local/qiime2_train.nf | 5 +++-- modules/local/qiime2_tree.nf | 5 +++-- 23 files changed, 65 insertions(+), 42 deletions(-) diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index e4cb923f..b8c09557 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -23,8 +23,9 @@ process QIIME2_ALPHARAREFACTION { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" maxdepth=\$(count_table_minmax_reads.py $stats maximum 2>&1) diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index ce580997..1d5b7686 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -24,8 +24,9 @@ process QIIME2_ANCOM_ASV { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime composition add-pseudocount \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index e5033d25..f05be617 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -22,8 +22,9 @@ process QIIME2_ANCOM_TAX { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" mkdir ancom # Sum data at the specified level diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index 73b6b13b..d3c3feda 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -25,8 +25,9 @@ process QIIME2_BARPLOT { suffix = setting ? "_${table.baseName}" : "" def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": "" """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime taxa barplot \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index e21c082c..be52e9bc 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -23,8 +23,9 @@ process QIIME2_CLASSIFY { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime feature-classifier classify-sklearn \\ --i-classifier ${trained_classifier} \\ diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 967685b2..2b992219 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -22,8 +22,9 @@ process QIIME2_DIVERSITY_ADONIS { script: def args = task.ext.args ?: '' """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime diversity adonis \\ --p-n-jobs $task.cpus \\ diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index efe1d669..4fb628dd 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -21,8 +21,9 @@ process QIIME2_DIVERSITY_ALPHA { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime diversity alpha-group-significance \\ --i-alpha-diversity ${core} \\ diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 044acaa5..7ae8e551 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -21,8 +21,9 @@ process QIIME2_DIVERSITY_BETA { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime diversity beta-group-significance \\ --i-distance-matrix ${core} \\ diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index ad7537b8..8852a9ce 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -21,8 +21,9 @@ process QIIME2_DIVERSITY_BETAORD { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" mkdir beta_diversity qiime emperor plot \\ diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index d248ae1a..7c104cfa 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -31,8 +31,9 @@ process QIIME2_DIVERSITY_CORE { # COMMENT: might be fixed in version after QIIME2 2023.5 export UNIFRAC_USE_GPU=N - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1) if [ \"\$mindepth\" -lt \"$mindepth\" ]; then mindepth=$mindepth; fi diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index 9f70976b..e96968ec 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -29,8 +29,9 @@ process QIIME2_EXPORT_ABSOLUTE { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" #produce raw count table in biom format "table/feature-table.biom" qiime tools export \\ diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index a8856728..697d53a3 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -20,8 +20,9 @@ process QIIME2_EXPORT_RELASV { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" #convert to relative abundances qiime feature-table relative-frequency \\ diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index 50de8e5e..a70f0579 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -23,8 +23,9 @@ process QIIME2_EXPORT_RELTAX { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" ##on several taxa level array=(\$(seq ${tax_agglom_min} 1 ${tax_agglom_max})) diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index 37c99989..d9bb373c 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -22,8 +22,9 @@ process QIIME2_EXTRACT { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" ### Import qiime tools import \\ diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index b6826132..b2346517 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -21,8 +21,9 @@ process QIIME2_FEATURETABLE_GROUP { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime feature-table filter-samples \\ --i-table "${table}" \\ diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index 5bb4a2cf..6a69c2e8 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -23,8 +23,9 @@ process QIIME2_FILTERSAMPLES { def args = task.ext.args ?: "--p-where \'${filter}<>\"\"\'" def prefix = task.ext.prefix ?: "${filter}" """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime feature-table filter-samples \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index 0590f3fd..df11ec08 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -28,8 +28,9 @@ process QIIME2_FILTERTAXA { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" if ! [ \"${exclude_taxa}\" = \"none\" ]; then #filter sequences diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf index 20fb526e..0fc2d2c5 100644 --- a/modules/local/qiime2_inasv.nf +++ b/modules/local/qiime2_inasv.nf @@ -21,7 +21,8 @@ process QIIME2_INASV { script: """ - export MPLCONFIGDIR="\${PWD}/HOME" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" # remove first line if needed sed '/^# Constructed from biom file/d' "$asv" > biom-table.txt diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf index 7c966a61..1aabf290 100644 --- a/modules/local/qiime2_inseq.nf +++ b/modules/local/qiime2_inseq.nf @@ -21,7 +21,8 @@ process QIIME2_INSEQ { script: """ - export MPLCONFIGDIR="\${PWD}/HOME" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime tools import \\ --input-path "$seq" \\ diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf index 6a208974..e2ef1ab8 100644 --- a/modules/local/qiime2_intax.nf +++ b/modules/local/qiime2_intax.nf @@ -23,7 +23,8 @@ process QIIME2_INTAX { script: def script_cmd = script ? "$script $tax" : "cp $tax tax.tsv" """ - export MPLCONFIGDIR="\${PWD}/HOME" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" $script_cmd diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf index ec4e85d1..6ee72a7c 100644 --- a/modules/local/qiime2_intree.nf +++ b/modules/local/qiime2_intree.nf @@ -21,7 +21,8 @@ process QIIME2_INTREE { script: """ - export MPLCONFIGDIR="\${PWD}/HOME" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime tools import \\ --type 'Phylogeny[Rooted]' \\ diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 892d510a..757fedf2 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -22,8 +22,9 @@ process QIIME2_TRAIN { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" #Train classifier qiime feature-classifier fit-classifier-naive-bayes \\ diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index 99ef87b4..c636af76 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -21,8 +21,9 @@ process QIIME2_TREE { script: """ - export XDG_CONFIG_HOME="\${PWD}/HOME" - export MPLCONFIGDIR="\${PWD}/HOME" + export XDG_CONFIG_HOME="/tmp/xdgconfig" + export MPLCONFIGDIR="/tmp/mplconfigdir" + export NUMBA_CACHE_DIR="/tmp/numbacache" qiime alignment mafft \\ --i-sequences ${repseq} \\ From ac61247d67ba249783cf2942781d2d12e132448b Mon Sep 17 00:00:00 2001 From: daniel Date: Tue, 7 Nov 2023 10:28:23 +0100 Subject: [PATCH 3/5] place XDG_CONFIG_HOME, MPLCONFIGDIR, NUMBA_CACHE_DIR in work directory instead of /tmp/ --- modules/local/qiime2_alphararefaction.nf | 6 +++--- modules/local/qiime2_ancom_asv.nf | 6 +++--- modules/local/qiime2_ancom_tax.nf | 6 +++--- modules/local/qiime2_barplot.nf | 6 +++--- modules/local/qiime2_classify.nf | 6 +++--- modules/local/qiime2_diversity_adonis.nf | 6 +++--- modules/local/qiime2_diversity_alpha.nf | 6 +++--- modules/local/qiime2_diversity_beta.nf | 6 +++--- modules/local/qiime2_diversity_betaord.nf | 6 +++--- modules/local/qiime2_diversity_core.nf | 6 +++--- modules/local/qiime2_export_absolute.nf | 6 +++--- modules/local/qiime2_export_relasv.nf | 6 +++--- modules/local/qiime2_export_reltax.nf | 6 +++--- modules/local/qiime2_extract.nf | 6 +++--- modules/local/qiime2_featuretable_group.nf | 6 +++--- modules/local/qiime2_filtersamples.nf | 6 +++--- modules/local/qiime2_filtertaxa.nf | 6 +++--- modules/local/qiime2_inasv.nf | 4 ++-- modules/local/qiime2_inseq.nf | 4 ++-- modules/local/qiime2_intax.nf | 4 ++-- modules/local/qiime2_intree.nf | 4 ++-- modules/local/qiime2_train.nf | 6 +++--- modules/local/qiime2_tree.nf | 6 +++--- 23 files changed, 65 insertions(+), 65 deletions(-) diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index b8c09557..8ed0cc13 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -23,9 +23,9 @@ process QIIME2_ALPHARAREFACTION { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" maxdepth=\$(count_table_minmax_reads.py $stats maximum 2>&1) diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index 1d5b7686..39e31e8d 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -24,9 +24,9 @@ process QIIME2_ANCOM_ASV { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime composition add-pseudocount \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index f05be617..ecaf2a1d 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -22,9 +22,9 @@ process QIIME2_ANCOM_TAX { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" mkdir ancom # Sum data at the specified level diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index d3c3feda..cbb933c6 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -25,9 +25,9 @@ process QIIME2_BARPLOT { suffix = setting ? "_${table.baseName}" : "" def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": "" """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime taxa barplot \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index be52e9bc..414f515b 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -23,9 +23,9 @@ process QIIME2_CLASSIFY { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime feature-classifier classify-sklearn \\ --i-classifier ${trained_classifier} \\ diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 2b992219..7fbef538 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -22,9 +22,9 @@ process QIIME2_DIVERSITY_ADONIS { script: def args = task.ext.args ?: '' """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime diversity adonis \\ --p-n-jobs $task.cpus \\ diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index 4fb628dd..ab9b2440 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -21,9 +21,9 @@ process QIIME2_DIVERSITY_ALPHA { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime diversity alpha-group-significance \\ --i-alpha-diversity ${core} \\ diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 7ae8e551..97f6c6ae 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -21,9 +21,9 @@ process QIIME2_DIVERSITY_BETA { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime diversity beta-group-significance \\ --i-distance-matrix ${core} \\ diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index 8852a9ce..59b7e6f6 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -21,9 +21,9 @@ process QIIME2_DIVERSITY_BETAORD { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" mkdir beta_diversity qiime emperor plot \\ diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index 7c104cfa..f3a775b3 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -31,9 +31,9 @@ process QIIME2_DIVERSITY_CORE { # COMMENT: might be fixed in version after QIIME2 2023.5 export UNIFRAC_USE_GPU=N - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1) if [ \"\$mindepth\" -lt \"$mindepth\" ]; then mindepth=$mindepth; fi diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index e96968ec..9f7d9d11 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -29,9 +29,9 @@ process QIIME2_EXPORT_ABSOLUTE { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" #produce raw count table in biom format "table/feature-table.biom" qiime tools export \\ diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index 697d53a3..65a6add5 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -20,9 +20,9 @@ process QIIME2_EXPORT_RELASV { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" #convert to relative abundances qiime feature-table relative-frequency \\ diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index a70f0579..32ea7d2d 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -23,9 +23,9 @@ process QIIME2_EXPORT_RELTAX { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" ##on several taxa level array=(\$(seq ${tax_agglom_min} 1 ${tax_agglom_max})) diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index d9bb373c..4b8a60b7 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -22,9 +22,9 @@ process QIIME2_EXTRACT { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" ### Import qiime tools import \\ diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index b2346517..887a1e75 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -21,9 +21,9 @@ process QIIME2_FEATURETABLE_GROUP { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime feature-table filter-samples \\ --i-table "${table}" \\ diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index 6a69c2e8..c9b279ef 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -23,9 +23,9 @@ process QIIME2_FILTERSAMPLES { def args = task.ext.args ?: "--p-where \'${filter}<>\"\"\'" def prefix = task.ext.prefix ?: "${filter}" """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime feature-table filter-samples \\ --i-table ${table} \\ diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index df11ec08..66013279 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -28,9 +28,9 @@ process QIIME2_FILTERTAXA { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" if ! [ \"${exclude_taxa}\" = \"none\" ]; then #filter sequences diff --git a/modules/local/qiime2_inasv.nf b/modules/local/qiime2_inasv.nf index 0fc2d2c5..68c08d58 100644 --- a/modules/local/qiime2_inasv.nf +++ b/modules/local/qiime2_inasv.nf @@ -21,8 +21,8 @@ process QIIME2_INASV { script: """ - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" # remove first line if needed sed '/^# Constructed from biom file/d' "$asv" > biom-table.txt diff --git a/modules/local/qiime2_inseq.nf b/modules/local/qiime2_inseq.nf index 1aabf290..a11529a3 100644 --- a/modules/local/qiime2_inseq.nf +++ b/modules/local/qiime2_inseq.nf @@ -21,8 +21,8 @@ process QIIME2_INSEQ { script: """ - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime tools import \\ --input-path "$seq" \\ diff --git a/modules/local/qiime2_intax.nf b/modules/local/qiime2_intax.nf index e2ef1ab8..cb7e7269 100644 --- a/modules/local/qiime2_intax.nf +++ b/modules/local/qiime2_intax.nf @@ -23,8 +23,8 @@ process QIIME2_INTAX { script: def script_cmd = script ? "$script $tax" : "cp $tax tax.tsv" """ - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" $script_cmd diff --git a/modules/local/qiime2_intree.nf b/modules/local/qiime2_intree.nf index 6ee72a7c..817e2a7b 100644 --- a/modules/local/qiime2_intree.nf +++ b/modules/local/qiime2_intree.nf @@ -21,8 +21,8 @@ process QIIME2_INTREE { script: """ - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime tools import \\ --type 'Phylogeny[Rooted]' \\ diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 757fedf2..09c70735 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -22,9 +22,9 @@ process QIIME2_TRAIN { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" #Train classifier qiime feature-classifier fit-classifier-naive-bayes \\ diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index c636af76..26711b04 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -21,9 +21,9 @@ process QIIME2_TREE { script: """ - export XDG_CONFIG_HOME="/tmp/xdgconfig" - export MPLCONFIGDIR="/tmp/mplconfigdir" - export NUMBA_CACHE_DIR="/tmp/numbacache" + export XDG_CONFIG_HOME="./xdgconfig" + export MPLCONFIGDIR="./mplconfigdir" + export NUMBA_CACHE_DIR="./numbacache" qiime alignment mafft \\ --i-sequences ${repseq} \\ From b6b7928185617ae2d1229a9fa1934eff9c748143 Mon Sep 17 00:00:00 2001 From: daniel Date: Tue, 7 Nov 2023 13:54:07 +0100 Subject: [PATCH 4/5] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index ddb0e72c..0fa237ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,6 +11,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 ### `Fixed` +- [#655](https://github.com/nf-core/ampliseq/pull/655) - Added `NUMBA_CACHE_DIR` to fix downstream analysis with QIIME2 that failed on some systems + ### `Dependencies` ### `Removed` From ac8b05c97d55f6996777d95f3083f86c39e4654e Mon Sep 17 00:00:00 2001 From: daniel Date: Tue, 7 Nov 2023 14:00:47 +0100 Subject: [PATCH 5/5] replace tab with 4 spaces --- modules/local/qiime2_alphararefaction.nf | 2 +- modules/local/qiime2_ancom_asv.nf | 2 +- modules/local/qiime2_ancom_tax.nf | 2 +- modules/local/qiime2_barplot.nf | 2 +- modules/local/qiime2_classify.nf | 2 +- modules/local/qiime2_diversity_adonis.nf | 2 +- modules/local/qiime2_diversity_alpha.nf | 2 +- modules/local/qiime2_diversity_beta.nf | 2 +- modules/local/qiime2_diversity_betaord.nf | 2 +- modules/local/qiime2_diversity_core.nf | 2 +- modules/local/qiime2_export_absolute.nf | 2 +- modules/local/qiime2_export_relasv.nf | 2 +- modules/local/qiime2_export_reltax.nf | 2 +- modules/local/qiime2_extract.nf | 2 +- modules/local/qiime2_featuretable_group.nf | 2 +- modules/local/qiime2_filtersamples.nf | 2 +- modules/local/qiime2_filtertaxa.nf | 2 +- modules/local/qiime2_train.nf | 2 +- modules/local/qiime2_tree.nf | 2 +- subworkflows/local/dada2_taxonomy_wf.nf | 2 +- 20 files changed, 20 insertions(+), 20 deletions(-) diff --git a/modules/local/qiime2_alphararefaction.nf b/modules/local/qiime2_alphararefaction.nf index 8ed0cc13..c37a8d57 100644 --- a/modules/local/qiime2_alphararefaction.nf +++ b/modules/local/qiime2_alphararefaction.nf @@ -24,7 +24,7 @@ process QIIME2_ALPHARAREFACTION { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" maxdepth=\$(count_table_minmax_reads.py $stats maximum 2>&1) diff --git a/modules/local/qiime2_ancom_asv.nf b/modules/local/qiime2_ancom_asv.nf index 39e31e8d..c5ee19a3 100644 --- a/modules/local/qiime2_ancom_asv.nf +++ b/modules/local/qiime2_ancom_asv.nf @@ -25,7 +25,7 @@ process QIIME2_ANCOM_ASV { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime composition add-pseudocount \\ diff --git a/modules/local/qiime2_ancom_tax.nf b/modules/local/qiime2_ancom_tax.nf index ecaf2a1d..1c5eccc8 100644 --- a/modules/local/qiime2_ancom_tax.nf +++ b/modules/local/qiime2_ancom_tax.nf @@ -23,7 +23,7 @@ process QIIME2_ANCOM_TAX { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" mkdir ancom diff --git a/modules/local/qiime2_barplot.nf b/modules/local/qiime2_barplot.nf index cbb933c6..cea39171 100644 --- a/modules/local/qiime2_barplot.nf +++ b/modules/local/qiime2_barplot.nf @@ -26,7 +26,7 @@ process QIIME2_BARPLOT { def metadata_cmd = metadata ? "--m-metadata-file ${metadata}": "" """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime taxa barplot \\ diff --git a/modules/local/qiime2_classify.nf b/modules/local/qiime2_classify.nf index 414f515b..a84bde40 100644 --- a/modules/local/qiime2_classify.nf +++ b/modules/local/qiime2_classify.nf @@ -24,7 +24,7 @@ process QIIME2_CLASSIFY { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime feature-classifier classify-sklearn \\ diff --git a/modules/local/qiime2_diversity_adonis.nf b/modules/local/qiime2_diversity_adonis.nf index 7fbef538..23016923 100644 --- a/modules/local/qiime2_diversity_adonis.nf +++ b/modules/local/qiime2_diversity_adonis.nf @@ -23,7 +23,7 @@ process QIIME2_DIVERSITY_ADONIS { def args = task.ext.args ?: '' """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime diversity adonis \\ diff --git a/modules/local/qiime2_diversity_alpha.nf b/modules/local/qiime2_diversity_alpha.nf index ab9b2440..5062b74b 100644 --- a/modules/local/qiime2_diversity_alpha.nf +++ b/modules/local/qiime2_diversity_alpha.nf @@ -22,7 +22,7 @@ process QIIME2_DIVERSITY_ALPHA { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime diversity alpha-group-significance \\ diff --git a/modules/local/qiime2_diversity_beta.nf b/modules/local/qiime2_diversity_beta.nf index 97f6c6ae..2e0d5864 100644 --- a/modules/local/qiime2_diversity_beta.nf +++ b/modules/local/qiime2_diversity_beta.nf @@ -22,7 +22,7 @@ process QIIME2_DIVERSITY_BETA { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime diversity beta-group-significance \\ diff --git a/modules/local/qiime2_diversity_betaord.nf b/modules/local/qiime2_diversity_betaord.nf index 59b7e6f6..ad6d8266 100644 --- a/modules/local/qiime2_diversity_betaord.nf +++ b/modules/local/qiime2_diversity_betaord.nf @@ -22,7 +22,7 @@ process QIIME2_DIVERSITY_BETAORD { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" mkdir beta_diversity diff --git a/modules/local/qiime2_diversity_core.nf b/modules/local/qiime2_diversity_core.nf index f3a775b3..d0569d87 100644 --- a/modules/local/qiime2_diversity_core.nf +++ b/modules/local/qiime2_diversity_core.nf @@ -32,7 +32,7 @@ process QIIME2_DIVERSITY_CORE { export UNIFRAC_USE_GPU=N export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" mindepth=\$(count_table_minmax_reads.py $stats minimum 2>&1) diff --git a/modules/local/qiime2_export_absolute.nf b/modules/local/qiime2_export_absolute.nf index 9f7d9d11..5e217f4a 100644 --- a/modules/local/qiime2_export_absolute.nf +++ b/modules/local/qiime2_export_absolute.nf @@ -30,7 +30,7 @@ process QIIME2_EXPORT_ABSOLUTE { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" #produce raw count table in biom format "table/feature-table.biom" diff --git a/modules/local/qiime2_export_relasv.nf b/modules/local/qiime2_export_relasv.nf index 65a6add5..85eedcda 100644 --- a/modules/local/qiime2_export_relasv.nf +++ b/modules/local/qiime2_export_relasv.nf @@ -21,7 +21,7 @@ process QIIME2_EXPORT_RELASV { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" #convert to relative abundances diff --git a/modules/local/qiime2_export_reltax.nf b/modules/local/qiime2_export_reltax.nf index 32ea7d2d..4b287917 100644 --- a/modules/local/qiime2_export_reltax.nf +++ b/modules/local/qiime2_export_reltax.nf @@ -24,7 +24,7 @@ process QIIME2_EXPORT_RELTAX { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" ##on several taxa level diff --git a/modules/local/qiime2_extract.nf b/modules/local/qiime2_extract.nf index 4b8a60b7..9e4bf2fa 100644 --- a/modules/local/qiime2_extract.nf +++ b/modules/local/qiime2_extract.nf @@ -23,7 +23,7 @@ process QIIME2_EXTRACT { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" ### Import diff --git a/modules/local/qiime2_featuretable_group.nf b/modules/local/qiime2_featuretable_group.nf index 887a1e75..eacb4d61 100644 --- a/modules/local/qiime2_featuretable_group.nf +++ b/modules/local/qiime2_featuretable_group.nf @@ -22,7 +22,7 @@ process QIIME2_FEATURETABLE_GROUP { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime feature-table filter-samples \\ diff --git a/modules/local/qiime2_filtersamples.nf b/modules/local/qiime2_filtersamples.nf index c9b279ef..01c9c11a 100644 --- a/modules/local/qiime2_filtersamples.nf +++ b/modules/local/qiime2_filtersamples.nf @@ -24,7 +24,7 @@ process QIIME2_FILTERSAMPLES { def prefix = task.ext.prefix ?: "${filter}" """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime feature-table filter-samples \\ diff --git a/modules/local/qiime2_filtertaxa.nf b/modules/local/qiime2_filtertaxa.nf index 66013279..3ea8828e 100644 --- a/modules/local/qiime2_filtertaxa.nf +++ b/modules/local/qiime2_filtertaxa.nf @@ -29,7 +29,7 @@ process QIIME2_FILTERTAXA { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" if ! [ \"${exclude_taxa}\" = \"none\" ]; then diff --git a/modules/local/qiime2_train.nf b/modules/local/qiime2_train.nf index 09c70735..48174e3c 100644 --- a/modules/local/qiime2_train.nf +++ b/modules/local/qiime2_train.nf @@ -23,7 +23,7 @@ process QIIME2_TRAIN { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" #Train classifier diff --git a/modules/local/qiime2_tree.nf b/modules/local/qiime2_tree.nf index 26711b04..a595b64a 100644 --- a/modules/local/qiime2_tree.nf +++ b/modules/local/qiime2_tree.nf @@ -22,7 +22,7 @@ process QIIME2_TREE { script: """ export XDG_CONFIG_HOME="./xdgconfig" - export MPLCONFIGDIR="./mplconfigdir" + export MPLCONFIGDIR="./mplconfigdir" export NUMBA_CACHE_DIR="./numbacache" qiime alignment mafft \\ diff --git a/subworkflows/local/dada2_taxonomy_wf.nf b/subworkflows/local/dada2_taxonomy_wf.nf index 9673b45e..c0e5a85d 100644 --- a/subworkflows/local/dada2_taxonomy_wf.nf +++ b/subworkflows/local/dada2_taxonomy_wf.nf @@ -83,7 +83,7 @@ workflow DADA2_TAXONOMY_WF { //set file name prefix for SH assignments if (!params.skip_dada_addspecies) { ASV_SH_name = "ASV_tax_species_SH" - } else { + } else { ASV_SH_name = "ASV_tax_SH" } //find SHs