From 06b6ee90f8d572f3b336375118add7b52e7591ab Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Tue, 19 Sep 2023 18:40:12 +0200 Subject: [PATCH 1/2] doc: since at least v2 we don't accept plain txt sequences --- docs/user/input-files.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/user/input-files.md b/docs/user/input-files.md index 9f4b11e82..742ecbd78 100644 --- a/docs/user/input-files.md +++ b/docs/user/input-files.md @@ -10,7 +10,7 @@ Nextclade Web (simple and advanced modes): accepted in "Sequences" drag & drop b Nextclade CLI and Nextalign CLI accept fasta inputs as one or multiple positional arguments. Accepts plain or compressed FASTA files. If a compressed fasta file is provided, it will be transparently decompressed. Supported compression formats: `gz`, `bz2`, `xz`, `zstd`. Decompressor is chosen based on file extension. If there's multiple input files, then different files can have different compression formats. If positional arguments provided, the plain fasta input is read from standard input (stdin). -Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) or plain text (one sequence per line). +Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) ## Reference (root) sequence From 469b7403853cd6ad3b7bc64f9e666336801d9330 Mon Sep 17 00:00:00 2001 From: Cornelius Roemer Date: Tue, 19 Sep 2023 18:44:37 +0200 Subject: [PATCH 2/2] doc: reference requires fasta since v2, txt not accepted --- docs/user/input-files.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/user/input-files.md b/docs/user/input-files.md index 742ecbd78..0d4ccad34 100644 --- a/docs/user/input-files.md +++ b/docs/user/input-files.md @@ -16,7 +16,7 @@ Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) Viral nucleotide sequence which serves as a reference for alignment and the analysis. Mutations are called relative to the reference sequence. It is expected to be the root of the [reference tree](#reference-tree). The best results are obtained when the reference sequence is a well-known consensus genome, of a very high quality, preferably complete and unambiguous (spans entire genome and has no ambiguous nucleotides). -Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) or plain text. The file is expected to contain only 1 sequence. +Accepted formats: [FASTA](https://en.wikipedia.org/wiki/FASTA_format) file containing exactly 1 sequence. Nextclade Web (advanced mode): accepted in "Root sequence" drag & drop box. A remote URL is also accepted in `input-root-sequence` URL parameter.