From 9e307db55dc8da168b9c18abacfe2af21fac9ebe Mon Sep 17 00:00:00 2001 From: Mike Marquet <40232542+mult1fractal@users.noreply.github.com> Date: Tue, 29 Nov 2022 10:04:59 +0100 Subject: [PATCH 1/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index c54289f..3c3e350 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ ![](https://img.shields.io/badge/uses-docker-blue.svg) ![](https://img.shields.io/badge/uses-singularity-yellow.svg) -[![Generic badge](https://img.shields.io/badge/Preprint-bioRxiv-red.svg)](https://www.biorxiv.org/content/10.1101/2020.07.24.219899v2) +[![Generic badge](https://img.shields.io/badge/Publication-blueviolet.svg)](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac110/6833029) [![Generic badge](https://img.shields.io/badge/Documentation-available-purple.svg)](https://mult1fractal.github.io/wtp-documentation/) [![Twitter Follow](https://img.shields.io/twitter/follow/gcloudChris.svg?style=social)](https://twitter.com/gcloudChris) From adb5c72f9dea5ee5b5a5b006799442620ce4254f Mon Sep 17 00:00:00 2001 From: Mike Marquet <40232542+mult1fractal@users.noreply.github.com> Date: Tue, 29 Nov 2022 10:06:36 +0100 Subject: [PATCH 2/7] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 3c3e350..2937750 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,7 @@ ![](https://img.shields.io/badge/uses-docker-blue.svg) ![](https://img.shields.io/badge/uses-singularity-yellow.svg) -[![Generic badge](https://img.shields.io/badge/Publication-blueviolet.svg)](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac110/6833029) +[![Generic badge](https://img.shields.io/badge/Publication-Gigascience-blueviolet.svg)](https://academic.oup.com/gigascience/article/doi/10.1093/gigascience/giac110/6833029) [![Generic badge](https://img.shields.io/badge/Documentation-available-purple.svg)](https://mult1fractal.github.io/wtp-documentation/) [![Twitter Follow](https://img.shields.io/twitter/follow/gcloudChris.svg?style=social)](https://twitter.com/gcloudChris) From cdcb18658131a3ce5cd74dcc52f51ca075621468 Mon Sep 17 00:00:00 2001 From: Mike Marquet <40232542+mult1fractal@users.noreply.github.com> Date: Tue, 29 Nov 2022 11:22:58 +0100 Subject: [PATCH 3/7] create citation.cff file issn not yet complete still ongiong volume --- CITATION.cff | 44 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 0000000..dcb194b --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,44 @@ +cff-version: 1.2.0 +message: "If you use this software, please cite it as below." +authors: + - family-names: "Marquet" + given-names: "Mike" + - family-names: "Hölzer" + given-names: "Martin" + - family-names: "Pletz" + given-names: "Mathias W." + - family-names: "Viehweger" + given-names: "Adrian" + - family-names: "Makarewicz" + given-names: "Oliwia" + - family-names: "Ehricht" + given-names: "Ralf" + - family-names: "Brandt" + given-names: "Christian" +title: "What the Phage: a scalable workflow for the identification and analysis of phage sequences" +version: v1.2.0 +date-released: 2022-11-18 +url: "https://github.com/replikation/What_the_Phage" +preferred-citation: + type: article + authors: + - family-names: "Marquet" + given-names: "Mike" + - family-names: "Hölzer" + given-names: "Martin" + - family-names: "Pletz" + given-names: "Mathias W." + - family-names: "Viehweger" + given-names: "Adrian" + - family-names: "Makarewicz" + given-names: "Oliwia" + - family-names: "Ehricht" + given-names: "Ralf" + - family-names: "Brandt" + given-names: "Christian" + doi: "10.1093/gigascience/giac110" + journal: "Gigascience" + month: 11 + title: "What the Phage: a scalable workflow for the identification and analysis of phage sequences" + year: 2022 + issn: 2047-217X From 9b5ab3232c503d47c45588116fd0f90e3dd6d7ad Mon Sep 17 00:00:00 2001 From: Mike Marquet <40232542+mult1fractal@users.noreply.github.com> Date: Tue, 29 Nov 2022 13:04:34 +0100 Subject: [PATCH 4/7] Update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 2937750..243cfd2 100644 --- a/README.md +++ b/README.md @@ -22,13 +22,13 @@ * These are extensively tested release versions of WtP * [releases of WtP are listed here](https://github.com/replikation/What_the_Phage/releases) -## Preprint: +## Publication: > **What the Phage: A scalable workflow for the identification and analysis of phage sequences** > > M. Marquet, M. Hölzer, M. W. Pletz, A. Viehweger, O. Makarewicz, R. Ehricht, C. Brandt > -> doi: https://doi.org/10.1101/2020.07.24.219899 +> doi: https://doi.org/10.1093/gigascience/giac110 # What is this repo From 28b6917545ad81aa210aae16886750f198c97396 Mon Sep 17 00:00:00 2001 From: Mike Marquet <40232542+mult1fractal@users.noreply.github.com> Date: Wed, 30 Nov 2022 11:10:14 +0100 Subject: [PATCH 5/7] Update CITATION.cff --- CITATION.cff | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index dcb194b..9f13368 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -1,20 +1,20 @@ cff-version: 1.2.0 message: "If you use this software, please cite it as below." authors: - - family-names: "Marquet" - given-names: "Mike" - - family-names: "Hölzer" - given-names: "Martin" - - family-names: "Pletz" - given-names: "Mathias W." - - family-names: "Viehweger" - given-names: "Adrian" - - family-names: "Makarewicz" - given-names: "Oliwia" - - family-names: "Ehricht" - given-names: "Ralf" - - family-names: "Brandt" - given-names: "Christian" +- family-names: "Marquet" + given-names: "Mike" +- family-names: "Hölzer" + given-names: "Martin" +- family-names: "Pletz" + given-names: "Mathias W." +- family-names: "Viehweger" + given-names: "Adrian" +- family-names: "Makarewicz" + given-names: "Oliwia" +- family-names: "Ehricht" + given-names: "Ralf" +- family-names: "Brandt" + given-names: "Christian" title: "What the Phage: a scalable workflow for the identification and analysis of phage sequences" version: v1.2.0 date-released: 2022-11-18 From 95f334807ff887a9a0f7a2e41b14a0cbbea967aa Mon Sep 17 00:00:00 2001 From: Mike Marquet <40232542+mult1fractal@users.noreply.github.com> Date: Wed, 30 Nov 2022 11:11:28 +0100 Subject: [PATCH 6/7] Update CITATION.cff --- CITATION.cff | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 9f13368..a58bb79 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -22,20 +22,20 @@ url: "https://github.com/replikation/What_the_Phage" preferred-citation: type: article authors: - - family-names: "Marquet" - given-names: "Mike" - - family-names: "Hölzer" - given-names: "Martin" - - family-names: "Pletz" - given-names: "Mathias W." - - family-names: "Viehweger" - given-names: "Adrian" - - family-names: "Makarewicz" - given-names: "Oliwia" - - family-names: "Ehricht" - given-names: "Ralf" - - family-names: "Brandt" - given-names: "Christian" + - family-names: "Marquet" + given-names: "Mike" + - family-names: "Hölzer" + given-names: "Martin" + - family-names: "Pletz" + given-names: "Mathias W." + - family-names: "Viehweger" + given-names: "Adrian" + - family-names: "Makarewicz" + given-names: "Oliwia" + - family-names: "Ehricht" + given-names: "Ralf" + - family-names: "Brandt" + given-names: "Christian" doi: "10.1093/gigascience/giac110" journal: "Gigascience" month: 11 From f613d87ac2799bee20cd8c83dd07d36fd884741e Mon Sep 17 00:00:00 2001 From: Mike Marquet <40232542+mult1fractal@users.noreply.github.com> Date: Thu, 26 Jan 2023 12:07:52 +0100 Subject: [PATCH 7/7] Update Heatmap_table.Rmd --- submodule_report/Heatmap_table.Rmd | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/submodule_report/Heatmap_table.Rmd b/submodule_report/Heatmap_table.Rmd index 58812ed..fea6c14 100644 --- a/submodule_report/Heatmap_table.Rmd +++ b/submodule_report/Heatmap_table.Rmd @@ -94,8 +94,8 @@ div.blue { background-color:#e6f0ff; border-radius: 5px; padding: 20px;} # Open your Linux-Terminal mkdir contigs_of_interest cd contigs_of_interest -# Copy the downloaded Phage prediction by contig table to the contig_IDs_of_interest -folder -# Copy the input_fasta to the contig_IDs_of_interest -folder +# Copy the downloaded Phage prediction by contig table to the contigs_of_interest -folder +# Copy the input_fasta to the contigs_of_interest -folder cp WtP_results/your_sample/Input_fasta/your_input_fasta.fa.gz /foo/bar/contigs_of_interest # Get contig IDs of interest tail -n+2 final_report.utf8.csv | tr -d '"' | cut -f2 -d"," > contig_IDs_of_interest.txt @@ -110,4 +110,4 @@ seqkit grep --pattern-file contig_IDs_of_interest.txt your_input_fasta.fa.gz > c -Back to top \ No newline at end of file +Back to top