From ed0e42289835dab5eb8daac8b80a1acf945eb484 Mon Sep 17 00:00:00 2001 From: luisas Date: Fri, 25 Oct 2024 17:30:19 +0200 Subject: [PATCH 1/5] change schema --- assets/schema_input.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/assets/schema_input.json b/assets/schema_input.json index c261ae5..133802a 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -7,7 +7,7 @@ "items": { "type": "object", "properties": { - "sequence": { + "id": { "type": "string", "pattern": "^\\S+$", "errorMessage": "Sequence name must be provided and cannot contain spaces", @@ -21,6 +21,6 @@ "errorMessage": "Fasta file must be provided, cannot contain spaces and must have extension '.fa' or '.fasta'" } }, - "required": ["sequence", "fasta"] + "required": ["id", "fasta"] } } From 6b2271c7524c826537e98911e353e1691a0ca54a Mon Sep 17 00:00:00 2001 From: luisas Date: Fri, 25 Oct 2024 17:35:53 +0200 Subject: [PATCH 2/5] update usage --- docs/usage.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 43b0d86..7e992f5 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -30,7 +30,7 @@ The samplesheet can have as many columns as you desire, however, there is a stri | Column | Description | | ---------- | --------------------------------------------------------------------------------------------------- | -| `sequence` | Custom sequence name. Spaces in sequence names are automatically converted to underscores (`_`). | +| `id` | Custom sequence name. Spaces in sequence names are automatically converted to underscores (`_`). | | `fasta` | Full path to fasta file for the provided sequence. File has to have the extension ".fasta" or "fa". | An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. From be2bf18228bc4bb09d7621707e193e1073847ca7 Mon Sep 17 00:00:00 2001 From: luisas Date: Fri, 25 Oct 2024 17:39:52 +0200 Subject: [PATCH 3/5] fix --- docs/usage.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index 7e992f5..cc7e0b1 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -28,10 +28,10 @@ T1026,https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testda The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 2 columns to match those defined in the table below: -| Column | Description | -| ---------- | --------------------------------------------------------------------------------------------------- | -| `id` | Custom sequence name. Spaces in sequence names are automatically converted to underscores (`_`). | -| `fasta` | Full path to fasta file for the provided sequence. File has to have the extension ".fasta" or "fa". | +| Column | Description | +| ------- | --------------------------------------------------------------------------------------------------- | +| `id` | Custom sequence name. Spaces in sequence names are automatically converted to underscores (`_`). | +| `fasta` | Full path to fasta file for the provided sequence. File has to have the extension ".fasta" or "fa". | An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. From bb1aa85f93f261e674167ff9da74d1cf4d74ff1f Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Mon, 28 Oct 2024 09:59:03 +0000 Subject: [PATCH 4/5] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3b38df4..3c631fb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -72,6 +72,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [[PR ##163](https://github.com/nf-core/proteinfold/pull/163)] - Fix full test CI. - [[#150]](https://github.com/nf-core/proteinfold/issues/150)] - Add thanks to the AWS Open Data Sponsorship program in `README.md`. - [[PR ##166](https://github.com/nf-core/proteinfold/pull/166)] - Create 2 different parameters for Colabfold and ESMfold number of recycles. +- [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from sequence,fasta to id,fasta. ### Parameters From a006829c380632454b1290a4e746b126e925c837 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Mon, 28 Oct 2024 11:10:02 +0100 Subject: [PATCH 5/5] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c631fb..2505139 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -72,7 +72,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [[PR ##163](https://github.com/nf-core/proteinfold/pull/163)] - Fix full test CI. - [[#150]](https://github.com/nf-core/proteinfold/issues/150)] - Add thanks to the AWS Open Data Sponsorship program in `README.md`. - [[PR ##166](https://github.com/nf-core/proteinfold/pull/166)] - Create 2 different parameters for Colabfold and ESMfold number of recycles. -- [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from sequence,fasta to id,fasta. +- [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from `sequence,fasta` to `id,fasta`. ### Parameters