diff --git a/public/images/contributing/creating_with_nf_core/git_log.svg b/public/images/contributing/creating_with_nf_core/git_log.svg
index 9b4e716f14..c1bdf713a7 100644
--- a/public/images/contributing/creating_with_nf_core/git_log.svg
+++ b/public/images/contributing/creating_with_nf_core/git_log.svg
@@ -19,27 +19,27 @@
font-weight: 700;
}
- .terminal-1718823819-matrix {
+ .terminal-1993354176-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1718823819-title {
+ .terminal-1993354176-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1718823819-r1 { fill: #c5c8c6 }
+ .terminal-1993354176-r1 { fill: #c5c8c6 }
-
+
-
+
@@ -51,11 +51,11 @@
-
+
-
- $ git log --oneline
-3029a70 initial template build from nf-core/tools, version 2.14.1
+
+ $ git log --oneline
+7b45b25 initial template build from nf-core/tools, version 2.14.1
diff --git a/public/images/contributing/creating_with_nf_core/nextflow_run_1.svg b/public/images/contributing/creating_with_nf_core/nextflow_run_1.svg
index 23663a109d..e88dd89b2f 100644
--- a/public/images/contributing/creating_with_nf_core/nextflow_run_1.svg
+++ b/public/images/contributing/creating_with_nf_core/nextflow_run_1.svg
@@ -19,278 +19,278 @@
font-weight: 700;
}
- .terminal-3751378249-matrix {
+ .terminal-1050508944-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-3751378249-title {
+ .terminal-1050508944-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-3751378249-r1 { fill: #c5c8c6 }
-.terminal-3751378249-r2 { fill: #868887 }
-.terminal-3751378249-r3 { fill: #98a84b }
-.terminal-3751378249-r4 { fill: #4b4e55 }
-.terminal-3751378249-r5 { fill: #608ab1 }
-.terminal-3751378249-r6 { fill: #d0b344 }
-.terminal-3751378249-r7 { fill: #98729f }
-.terminal-3751378249-r8 { fill: #c5c8c6;font-weight: bold }
+ .terminal-1050508944-r1 { fill: #c5c8c6 }
+.terminal-1050508944-r2 { fill: #868887 }
+.terminal-1050508944-r3 { fill: #98a84b }
+.terminal-1050508944-r4 { fill: #4b4e55 }
+.terminal-1050508944-r5 { fill: #608ab1 }
+.terminal-1050508944-r6 { fill: #d0b344 }
+.terminal-1050508944-r7 { fill: #98729f }
+.terminal-1050508944-r8 { fill: #c5c8c6;font-weight: bold }
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- nextflow run
+ nextflow run
-
+
-
- $ nextflow run nf-core-demo/ -profile test,docker --outdir test_results
-N E X T F L O W ~ version 24.04.1
-Launching `nf-core-demo/main.nf` [wise_pasteur] DSL2 - revision: 9539a5d3d4
-Downloading plugin nf-validation@1.1.3
-WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
-
-
-------------------------------------------------------
-,--./,-.
- ___ __ __ __ ___ /,-._.--~'
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
-`._,._,'
- nf-core/demo v1.0dev
-------------------------------------------------------
-Core Nextflow options
-runName : wise_pasteur
-containerEngine : docker
-launchDir : /home/runner/work/website/website
-workDir : /home/runner/work/website/website/work
-projectDir : /home/runner/work/website/website/nf-core-demo
-userName : runner
-profile : test,docker
-configFiles :
-
-Input/output options
-input : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
-outdir : test_results
-
-Reference genome options
-genome : R64-1-1
-fasta : s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa
-
-Institutional config options
-config_profile_name : Test profile
-config_profile_description: Minimal test dataset to check pipeline function
-
-Max job request options
-max_cpus : 2
-max_memory : 6.GB
-max_time : 6.h
-
-!! Only displaying parameters that differ from the pipeline defaults !!
-------------------------------------------------------
-If you use nf-core/demo for your analysis please cite:
-
-* The pipeline
-
-* The nf-core framework
- https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
- https://github.com/nf-core/demo/blob/master/CITATIONS.md
-------------------------------------------------------
-[db/57e950] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE1_PE)
-[78/a98708] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE3_SE)
-[ae/1f6353] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE)
-[cd/057d43] Submitted process > NFCORE_DEMO:DEMO:MULTIQC
--[nf-core/demo] Pipeline completed successfully-
+
+ $ nextflow run nf-core-demo/ -profile test,docker --outdir test_results
+N E X T F L O W ~ version 24.04.4
+Launching `nf-core-demo/main.nf` [high_thompson] DSL2 - revision: 9539a5d3d4
+Downloading plugin nf-validation@1.1.3
+WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`
+
+
+------------------------------------------------------
+,--./,-.
+ ___ __ __ __ ___ /,-._.--~'
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+`._,._,'
+ nf-core/demo v1.0dev
+------------------------------------------------------
+Core Nextflow options
+runName : high_thompson
+containerEngine : docker
+launchDir : /home/runner/work/website/website
+workDir : /home/runner/work/website/website/work
+projectDir : /home/runner/work/website/website/nf-core-demo
+userName : runner
+profile : test,docker
+configFiles :
+
+Input/output options
+input : https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv
+outdir : test_results
+
+Reference genome options
+genome : R64-1-1
+fasta : s3://ngi-igenomes/igenomes//Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa
+
+Institutional config options
+config_profile_name : Test profile
+config_profile_description: Minimal test dataset to check pipeline function
+
+Max job request options
+max_cpus : 2
+max_memory : 6.GB
+max_time : 6.h
+
+!! Only displaying parameters that differ from the pipeline defaults !!
+------------------------------------------------------
+If you use nf-core/demo for your analysis please cite:
+
+* The pipeline
+
+* The nf-core framework
+ https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+ https://github.com/nf-core/demo/blob/master/CITATIONS.md
+------------------------------------------------------
+[b8/43305d] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE2_PE)
+[13/1d0b6f] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE1_PE)
+[39/0cad3e] Submitted process > NFCORE_DEMO:DEMO:FASTQC (SAMPLE3_SE)
+[1a/0afa0c] Submitted process > NFCORE_DEMO:DEMO:MULTIQC
+-[nf-core/demo] Pipeline completed successfully-
diff --git a/public/images/contributing/creating_with_nf_core/nextflow_run_help.svg b/public/images/contributing/creating_with_nf_core/nextflow_run_help.svg
index fa77411c56..a3aff5e1f0 100644
--- a/public/images/contributing/creating_with_nf_core/nextflow_run_help.svg
+++ b/public/images/contributing/creating_with_nf_core/nextflow_run_help.svg
@@ -19,158 +19,158 @@
font-weight: 700;
}
- .terminal-1785758157-matrix {
+ .terminal-2966389272-matrix {
font-family: Fira Code, monospace;
font-size: 20px;
line-height: 24.4px;
font-variant-east-asian: full-width;
}
- .terminal-1785758157-title {
+ .terminal-2966389272-title {
font-size: 18px;
font-weight: bold;
font-family: arial;
}
- .terminal-1785758157-r1 { fill: #c5c8c6 }
-.terminal-1785758157-r2 { fill: #868887 }
-.terminal-1785758157-r3 { fill: #98a84b }
-.terminal-1785758157-r4 { fill: #4b4e55 }
-.terminal-1785758157-r5 { fill: #608ab1 }
-.terminal-1785758157-r6 { fill: #d0b344 }
-.terminal-1785758157-r7 { fill: #98729f }
-.terminal-1785758157-r8 { fill: #68a0b3 }
-.terminal-1785758157-r9 { fill: #c5c8c6;font-weight: bold;text-decoration: underline; }
+ .terminal-2966389272-r1 { fill: #c5c8c6 }
+.terminal-2966389272-r2 { fill: #868887 }
+.terminal-2966389272-r3 { fill: #98a84b }
+.terminal-2966389272-r4 { fill: #4b4e55 }
+.terminal-2966389272-r5 { fill: #608ab1 }
+.terminal-2966389272-r6 { fill: #d0b344 }
+.terminal-2966389272-r7 { fill: #98729f }
+.terminal-2966389272-r8 { fill: #68a0b3 }
+.terminal-2966389272-r9 { fill: #c5c8c6;font-weight: bold;text-decoration: underline; }
-
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@@ -182,52 +182,52 @@
-
+
-
- $ nextflow run nf-core-demo/ --help
-N E X T F L O W ~ version 24.04.1
-Launching `nf-core-demo/main.nf` [gloomy_cori] DSL2 - revision: 50393df5b8
-
-
-------------------------------------------------------
-,--./,-.
- ___ __ __ __ ___ /,-._.--~'
- |\ | |__ __ / ` / \ |__) |__ } {
- | \| | \__, \__/ | \ |___ \`-._,-`-,
-`._,._,'
- nf-core/demo v1.0dev
-------------------------------------------------------
-Typical pipeline command:
-
-nextflow run nf-core/demo -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>
-
-Input/output options
- --input [string] Path to comma-separated file containing information about the samples in the experiment.
- --outdir [string] The output directory where the results will be saved. You have to use absolute paths to storage on Cloud
- infrastructure.
- --email [string] Email address for completion summary.
- --multiqc_title [string] MultiQC report title. Printed as page header, used for filename if not otherwise specified.
-
-Reference genome options
- --genome [string] Name of iGenomes reference.
- --fasta [string] Path to FASTA genome file.
-
-Generic options
- --multiqc_methods_description [string] Custom MultiQC yaml file containing HTML including a methods description.
-
- !! Hiding 25 params, use --validationShowHiddenParams to show them !!
-------------------------------------------------------
-If you use nf-core/demo for your analysis please cite:
-
-* The pipeline
-
-* The nf-core framework
- https://doi.org/10.1038/s41587-020-0439-x
-
-* Software dependencies
- https://github.com/nf-core/demo/blob/master/CITATIONS.md
-------------------------------------------------------
+
+ $ nextflow run nf-core-demo/ --help
+N E X T F L O W ~ version 24.04.4
+Launching `nf-core-demo/main.nf` [adoring_pare] DSL2 - revision: 50393df5b8
+
+
+------------------------------------------------------
+,--./,-.
+ ___ __ __ __ ___ /,-._.--~'
+ |\ | |__ __ / ` / \ |__) |__ } {
+ | \| | \__, \__/ | \ |___ \`-._,-`-,
+`._,._,'
+ nf-core/demo v1.0dev
+------------------------------------------------------
+Typical pipeline command:
+
+nextflow run nf-core/demo -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>
+
+Input/output options
+ --input [string] Path to comma-separated file containing information about the samples in the experiment.
+ --outdir [string] The output directory where the results will be saved. You have to use absolute paths to storage on Cloud
+ infrastructure.
+ --email [string] Email address for completion summary.
+ --multiqc_title [string] MultiQC report title. Printed as page header, used for filename if not otherwise specified.
+
+Reference genome options
+ --genome [string] Name of iGenomes reference.
+ --fasta [string] Path to FASTA genome file.
+
+Generic options
+ --multiqc_methods_description [string] Custom MultiQC yaml file containing HTML including a methods description.
+
+ !! Hiding 25 params, use --validationShowHiddenParams to show them !!
+------------------------------------------------------
+If you use nf-core/demo for your analysis please cite:
+
+* The pipeline
+
+* The nf-core framework
+ https://doi.org/10.1038/s41587-020-0439-x
+
+* Software dependencies
+ https://github.com/nf-core/demo/blob/master/CITATIONS.md
+------------------------------------------------------
diff --git a/public/images/contributing/creating_with_nf_core/nextflow_run_no_outdir.svg b/public/images/contributing/creating_with_nf_core/nextflow_run_no_outdir.svg
index a83bb9b7f3..24c983c52b 100644
--- a/public/images/contributing/creating_with_nf_core/nextflow_run_no_outdir.svg
+++ b/public/images/contributing/creating_with_nf_core/nextflow_run_no_outdir.svg
@@ -1,4 +1,4 @@
-