From 3acd45cfe50a1062125e038eb02ee22fc7fee68e Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Wed, 7 Sep 2022 14:42:09 +0200 Subject: [PATCH 1/3] docs: mention that a log file with a fixed file name is always created --- docs/source/03_02_output_data.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/source/03_02_output_data.md b/docs/source/03_02_output_data.md index 57ea1ed3..43fff6eb 100755 --- a/docs/source/03_02_output_data.md +++ b/docs/source/03_02_output_data.md @@ -109,6 +109,9 @@ The following table describes each of the annotations in the output: | Hex_alignment_score_MHCI | the alignment score by HEX for ` Best_affinity_MHCI_epitope ` | HEX | | Hex_alignment_score_MHCII | the alignment score by HEX for ` Best_affinity_MHCII_epitope` | HEX | +In addition, a log file with the suffix "*_neoantigen_candidates_annotated.log*" +is always created. + ### Tabular format An output table with the suffix "*_neoantigen_candidates_annotated.tsv*" is created. From 0795a873ec47e1533ca44cd2ec2856b0771a5946 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Wed, 7 Sep 2022 14:44:54 +0200 Subject: [PATCH 2/3] include info that all logging is always appended --- docs/source/03_02_output_data.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/source/03_02_output_data.md b/docs/source/03_02_output_data.md index 43fff6eb..db3ccb83 100755 --- a/docs/source/03_02_output_data.md +++ b/docs/source/03_02_output_data.md @@ -109,8 +109,8 @@ The following table describes each of the annotations in the output: | Hex_alignment_score_MHCI | the alignment score by HEX for ` Best_affinity_MHCI_epitope ` | HEX | | Hex_alignment_score_MHCII | the alignment score by HEX for ` Best_affinity_MHCII_epitope` | HEX | -In addition, a log file with the suffix "*_neoantigen_candidates_annotated.log*" -is always created. +In addition, all logging output is appended to a log file with the suffix +"*_neoantigen_candidates_annotated.log*". ### Tabular format From 9f416fa3189461c2f8334f65bd617c474d7642a7 Mon Sep 17 00:00:00 2001 From: David Laehnemann Date: Wed, 7 Sep 2022 23:00:25 +0200 Subject: [PATCH 3/3] adjust wording to reflect the correct file naming --- docs/source/03_02_output_data.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/docs/source/03_02_output_data.md b/docs/source/03_02_output_data.md index db3ccb83..3470990a 100755 --- a/docs/source/03_02_output_data.md +++ b/docs/source/03_02_output_data.md @@ -110,7 +110,8 @@ The following table describes each of the annotations in the output: | Hex_alignment_score_MHCII | the alignment score by HEX for ` Best_affinity_MHCII_epitope` | HEX | In addition, all logging output is appended to a log file with the suffix -"*_neoantigen_candidates_annotated.log*". +"*/.log*", where the folder is set by `--output-folder` and the +prefix can be set with `--output-prefix`. ### Tabular format