From 90bc25f0e6826b2640637e326f44b2c217624dc9 Mon Sep 17 00:00:00 2001 From: vsc10579 Date: Tue, 12 Mar 2024 13:10:20 +0100 Subject: [PATCH 1/2] fix path issue --- magic_hydra.sh | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/magic_hydra.sh b/magic_hydra.sh index 0214024..5be57ba 100755 --- a/magic_hydra.sh +++ b/magic_hydra.sh @@ -1,6 +1,6 @@ #!/bin/bash -module load Nextflow/23.04.2 -house=$VSC_SCRATCH/simsapiper +module load Nextflow/23.10.0 +house=$VSC_SCRATCH_VO_USER/simsapiper data=toy_example now=`date +"%Y_%m_%d_%H_%M_%S"` output_name=${data}_${now}_test @@ -8,7 +8,7 @@ output_folder=$house/results/$output_name mkdir -p $house/results mkdir -p $output_folder nextflow run simsapiper.nf \ - -profile hydra,withsingularity \ + -profile hydra \ --data $house/$data/data \ --magic \ --outFolder $output_folder \ @@ -16,3 +16,5 @@ nextflow run simsapiper.nf \ |& tee $output_folder/run_report_$output_name.nflog sessionName=$(sed -n '2s/.*\[\(.*\)\].*/\1/p' $output_folder/run_report_$output_name.nflog) nextflow log | grep $sessionName >> $output_folder/run_report_$output_name.nflog + +#screen -S nextflowalign bash -c ./magic_hydra.sh \ No newline at end of file From 382c14251d2110648913d41b735075b973d40fb8 Mon Sep 17 00:00:00 2001 From: charlieccp <74074591+charlieccp@users.noreply.github.com> Date: Tue, 19 Mar 2024 18:03:06 +0100 Subject: [PATCH 2/2] clarify reordering --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 4ca8aba..df7f522 100644 --- a/README.md +++ b/README.md @@ -97,7 +97,7 @@ nextflow run simsapiper.nf | --dssp | Map DSSP code to alignment | false | | | --squeeze | Squeeze alignment towards conserved 2nd structure elements
Find all possible 2nd structure [elements](https://ssbio.readthedocs.io/en/latest/instructions/dssp.html) | false | "H,E" | | --squeezePerc | Set minimal occurence % of anchor element in MSA | 80 | | -| --reorder | Order final MSA by input file order | false | "gamma.fasta,delta.fasta”
“true” for alphabetical order | +| --reorder | Order final MSA by input file order | false | | | --convertMSA | Covert final MSA file from fasta to selected file format | false | "clustal" | | --magic | Launch a run with recommended settings for all parameters | false | | @@ -437,7 +437,7 @@ Common Issues: ## 8. Reorder MSA (--reorder) Output: `results/outFolder/reordered_*_merged_finalmsa_alignment.fasta` -- Order MSA according to the order of sequences in the input files in alphabetical order or by user defined order **--reorder "gamma.fasta,delta.fasta”** +- Order MSA according to the order of sequences in the input files. If more then one sequence input file is provided, order MSQ based on the order given in the files organized alphabetically. Instead of alphabetically, can also select explicitly how to organize the files with **--reorder "gamma.fasta,delta.fasta”** ## 9. Convert MSA Output: `results/outFolder/seqs/converted_*_merged_finalmsa_alignment.fasta`