test v0.1.12

pirl-unc · Nov 26, 2024 · f5b002e · f5b002e
1 parent 8c28ab0
commit f5b002e
Showing 1 changed file with 4 additions and 5 deletions.
diff --git a/...xuslib/pipelines/variant_calling/long_read_dna_variant_calling_savana/README.md b/...xuslib/pipelines/variant_calling/long_read_dna_variant_calling_savana/README.md
@@ -20,8 +20,8 @@ nexus run --nf-workflow long_read_dna_variant_calling_savana.nf \
     -c NEXTFLOW_CONFIG_FILE \
     -w WORK_DIR \
     --samples_tsv_file SAMPLES_TSV_FILE \
+    --contigs_txt_file CONTIGS_TXT_FILE \
     --output_dir OUTPUT_DIR \
-    --contigs_file CONTIGS_FILE \
     --reference_genome_fasta_file REFERENCE_GENOME_FASTA_FILE \
     --reference_genome_fasta_fai_file REFERENCE_GENOME_FASTA_FAI_FILE \
     --custom_params_file CUSTOM_PARAMS_FILE \
@@ -40,9 +40,8 @@ usage: nexus run --nf-workflow long_read_dna_variant_calling_savana.nf [required
 required arguments:
     -c                                  :   Nextflow .config file.
     -w                                  :   Nextflow work directory path.
-    --samples_tsv_file                  :   TSV file with the following columns: 
-                                            'sample_id', 'tumor_bam_file', 'tumor_bam_bai_file', 'normal_bam_file', 'normal_bam_bai_file'.
-    --contigs_txt_file                  :   TXT file with each contig name (e.g. chr1) in a new line.
+    --samples_tsv_file                  :   TSV file with the following columns: 'sample_id', 'tumor_bam_file', 'tumor_bam_bai_file', 'normal_bam_file', 'normal_bam_bai_file'.
+    --contigs_txt_file                  :   TXT file with each contig name in a new line.
     --output_dir                        :   Directory to which output files will be copied.
 
 optional arguments:
@@ -72,7 +71,7 @@ optional arguments:
 | normal_bam_file     | Full path to normal `bam` file     |
 | normal_bam_bai_file | Full path to normal `bam.bai` file |
 
-`--contigs_file`
+`--contigs_txt_file`
 * Savana `run` command `--contigs` file can be found in /datastore/lbcfs/collaborations/pirl/seqdata/tool-resources/savana/ on LBG.
 
 `--reference_genome_fasta_file`