From fe03305655b6a30eccefc2d57f4bab2c9c3e36ec Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Thu, 18 Jul 2024 10:44:44 +0100 Subject: [PATCH 1/4] conf/test_full.config Spelling mistake --- conf/test_full.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index 42292fd..f82aba5 100755 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -25,7 +25,7 @@ params { sample = "testing" input = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta" longread = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/fasta/" - cram = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima/full/" + cram = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/full/" sample = "CurationPretextTest" teloseq = "TTAGGG" aligner = "bwamem2" From 46f54e718dad173a1718dfd73cfafbee25a7cd62 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Thu, 18 Jul 2024 10:53:35 +0100 Subject: [PATCH 2/4] adding the LSF test profile to the config --- nextflow.config | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 259f638..68f72d9 100755 --- a/nextflow.config +++ b/nextflow.config @@ -160,7 +160,8 @@ profiles { executor.cpus = 16 executor.memory = 60.GB } - test { includeConfig 'conf/test.config' } + test { includeConfig 'conf/test.config' } + test_full { includeConfig 'conf/test_full.config } } // Export these variables to prevent local Python/R libraries from conflicting with those in the container From 59ea62829dacd2091f75e0750aa4c664295fe287 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Thu, 18 Jul 2024 11:14:29 +0100 Subject: [PATCH 3/4] Missing quote --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 68f72d9..93bd96e 100755 --- a/nextflow.config +++ b/nextflow.config @@ -161,7 +161,7 @@ profiles { executor.memory = 60.GB } test { includeConfig 'conf/test.config' } - test_full { includeConfig 'conf/test_full.config } + test_full { includeConfig 'conf/test_full.config' } } // Export these variables to prevent local Python/R libraries from conflicting with those in the container From c51a3aca1148ffaf0d5d3ab39f10d76129c35157 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Thu, 18 Jul 2024 11:27:25 +0100 Subject: [PATCH 4/4] Changing to the Tiny Test Data --- conf/test_full.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/conf/test_full.config b/conf/test_full.config index f82aba5..50206e4 100755 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -23,9 +23,9 @@ params { max_time = '6.h' sample = "testing" - input = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/assembly/draft/DF5033.hifiasm.noTelos.20211120/DF5033.noTelos.hifiasm.purged.noCont.noMito.fasta" - longread = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/pacbio/fasta/" - cram = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValSmallData/Oscheius_DF5033/genomic_data/nxOscSpes1/hic-arima2/full/" + input = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValTinyData/assembly/draft/grTriPseu1.fa" + longread = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValTinyData/genomic_data/pacbio/" + cram = "/lustre/scratch123/tol/resources/treeval/treeval-testdata/TreeValTinyData/genomic_data/hic-arima/" sample = "CurationPretextTest" teloseq = "TTAGGG" aligner = "bwamem2"