From 8575090df540f19bc2bed4734a348446a6aac8e9 Mon Sep 17 00:00:00 2001 From: d4straub Date: Mon, 18 Mar 2024 10:19:57 +0100 Subject: [PATCH] prevent execution with conda --- modules/local/sidle_align.nf | 4 ++++ modules/local/sidle_dbextract.nf | 4 ++++ modules/local/sidle_dbfilt.nf | 4 ++++ modules/local/sidle_dbrecon.nf | 4 ++++ modules/local/sidle_filttax.nf | 4 ++++ modules/local/sidle_in.nf | 4 ++++ modules/local/sidle_indb.nf | 4 ++++ modules/local/sidle_indbaligned.nf | 4 ++++ modules/local/sidle_seqrecon.nf | 4 ++++ modules/local/sidle_tablerecon.nf | 4 ++++ modules/local/sidle_taxrecon.nf | 4 ++++ modules/local/sidle_treerecon.nf | 4 ++++ modules/local/sidle_trim.nf | 4 ++++ 13 files changed, 52 insertions(+) diff --git a/modules/local/sidle_align.nf b/modules/local/sidle_align.nf index c98f955e..15a3467b 100644 --- a/modules/local/sidle_align.nf +++ b/modules/local/sidle_align.nf @@ -15,6 +15,10 @@ process SIDLE_ALIGN { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.region}" def primerfw = "${meta.fw_primer}" diff --git a/modules/local/sidle_dbextract.nf b/modules/local/sidle_dbextract.nf index c57597e3..91f3635e 100644 --- a/modules/local/sidle_dbextract.nf +++ b/modules/local/sidle_dbextract.nf @@ -17,6 +17,10 @@ process SIDLE_DBEXTRACT { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.region}" def primerfw = "${meta.fw_primer}" diff --git a/modules/local/sidle_dbfilt.nf b/modules/local/sidle_dbfilt.nf index b5bfd93e..60b4b30f 100644 --- a/modules/local/sidle_dbfilt.nf +++ b/modules/local/sidle_dbfilt.nf @@ -16,6 +16,10 @@ process SIDLE_DBFILT { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' """ diff --git a/modules/local/sidle_dbrecon.nf b/modules/local/sidle_dbrecon.nf index 83c87264..18a819b3 100644 --- a/modules/local/sidle_dbrecon.nf +++ b/modules/local/sidle_dbrecon.nf @@ -18,6 +18,10 @@ process SIDLE_DBRECON { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def db_input = "" // sort the input so that the regions are sorted by sequence diff --git a/modules/local/sidle_filttax.nf b/modules/local/sidle_filttax.nf index 00133e64..52804b8a 100644 --- a/modules/local/sidle_filttax.nf +++ b/modules/local/sidle_filttax.nf @@ -17,6 +17,10 @@ process SIDLE_FILTTAX { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ #!/usr/bin/env Rscript diff --git a/modules/local/sidle_in.nf b/modules/local/sidle_in.nf index 1f1d5360..4eddef41 100644 --- a/modules/local/sidle_in.nf +++ b/modules/local/sidle_in.nf @@ -15,6 +15,10 @@ process SIDLE_IN { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.region}" """ diff --git a/modules/local/sidle_indb.nf b/modules/local/sidle_indb.nf index 33367313..f91a21ac 100644 --- a/modules/local/sidle_indb.nf +++ b/modules/local/sidle_indb.nf @@ -16,6 +16,10 @@ process SIDLE_INDB { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ export XDG_CONFIG_HOME="./xdgconfig" export MPLCONFIGDIR="./mplconfigdir" diff --git a/modules/local/sidle_indbaligned.nf b/modules/local/sidle_indbaligned.nf index e37b169a..4029d697 100644 --- a/modules/local/sidle_indbaligned.nf +++ b/modules/local/sidle_indbaligned.nf @@ -14,6 +14,10 @@ process SIDLE_INDBALIGNED { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' """ export XDG_CONFIG_HOME="./xdgconfig" diff --git a/modules/local/sidle_seqrecon.nf b/modules/local/sidle_seqrecon.nf index 6330e376..38fa742d 100644 --- a/modules/local/sidle_seqrecon.nf +++ b/modules/local/sidle_seqrecon.nf @@ -19,6 +19,10 @@ process SIDLE_SEQRECON { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ #https://q2-sidle.readthedocs.io/en/latest/reconstruction.html#reconstructing-the-phylogenetic-tree #https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/4 for db_aligned_sequences diff --git a/modules/local/sidle_tablerecon.nf b/modules/local/sidle_tablerecon.nf index cd6d14f3..fc6ba9ee 100644 --- a/modules/local/sidle_tablerecon.nf +++ b/modules/local/sidle_tablerecon.nf @@ -21,6 +21,10 @@ process SIDLE_TABLERECON { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def region_input = "" // sort the input so that the regions are sorted by sequence diff --git a/modules/local/sidle_taxrecon.nf b/modules/local/sidle_taxrecon.nf index 0172f6c2..5503cf65 100644 --- a/modules/local/sidle_taxrecon.nf +++ b/modules/local/sidle_taxrecon.nf @@ -17,6 +17,10 @@ process SIDLE_TAXRECON { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' """ #https://q2-sidle.readthedocs.io/en/latest/reconstruction.html#taxonomic-reconstruction diff --git a/modules/local/sidle_treerecon.nf b/modules/local/sidle_treerecon.nf index 0d12be82..91838e3e 100644 --- a/modules/local/sidle_treerecon.nf +++ b/modules/local/sidle_treerecon.nf @@ -17,6 +17,10 @@ process SIDLE_TREERECON { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } """ # https://q2-sidle.readthedocs.io/en/latest/reconstruction.html#reconstructing-the-phylogenetic-tree # required: SEPP file https://forum.qiime2.org/t/sidle-tutorial-missing-aligned-sequence-file/20604/8 diff --git a/modules/local/sidle_trim.nf b/modules/local/sidle_trim.nf index e4db979d..7727f837 100644 --- a/modules/local/sidle_trim.nf +++ b/modules/local/sidle_trim.nf @@ -16,6 +16,10 @@ process SIDLE_TRIM { task.ext.when == null || task.ext.when script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "Sidle in QIIME2 does not support Conda. Please use Docker / Singularity / Podman instead." + } def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.region}" def primerfw = "${meta.fw_primer}"