From 9fe7a4f8d04374cb2c4a70e58db60a3bc5f6bb0d Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 24 Oct 2022 22:15:35 +0000 Subject: [PATCH 1/3] Add note why no download possible --- docs/usage.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/docs/usage.md b/docs/usage.md index 1bfa8051..bc6c3a4b 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -32,10 +32,12 @@ Different parameters can be set for the two supported databases. By default `miR If MirGeneDB should be used instead it needs to be specified using `--mirgenedb` and use the parameters below . -- `mirgenedb_gff`: The data can not be downloaded automatically, thus the user needs to supply the gff file for either his species, or all species downloaded from `https://mirgenedb.org/download`. The total set will automatically be subsetted to the species specified with `--mirgenedb_species`. +- `mirgenedb_gff`: The data can not be downloaded automatically (URLs are created with short term tokens in it), thus the user needs to supply the gff file for either his species, or all species downloaded from `https://mirgenedb.org/download`. The total set will automatically be subsetted to the species specified with `--mirgenedb_species`. - `mirgenedb_mature`: points to the FASTA file of mature miRNA sequences. Download from `https://mirgenedb.org/download`. - `mirgenedb_hairpin`: points to the FASTA file of precursor miRNA sequences. Download from `https://mirgenedb.org/download`. Note that MirGeneDB does not have a dedicated `hairpin` file, but the `Precursor sequences` are to be used. + + ### Genome - `fasta`: the reference genome FASTA file From 2ff08d92da17f7ae78da85380f959dc3e74aa3e6 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 24 Oct 2022 22:20:23 +0000 Subject: [PATCH 2/3] Adjust = to be same everywhere --- nextflow.config | 208 ++++++++++++++++++++++++------------------------ 1 file changed, 104 insertions(+), 104 deletions(-) diff --git a/nextflow.config b/nextflow.config index b1b24dbc..759cf40d 100644 --- a/nextflow.config +++ b/nextflow.config @@ -10,84 +10,84 @@ params { // Input options - input = null + input = null // Workflow flags - protocol = 'illumina' + protocol = 'illumina' // References - genome = null - igenomes_base = 's3://ngi-igenomes/igenomes' - igenomes_ignore = false - mirna_gtf = null - mature = "https://mirbase.org/ftp/CURRENT/mature.fa.gz" - hairpin = "https://mirbase.org/ftp/CURRENT/hairpin.fa.gz" - mirgenedb = false - mirgenedb_mature = null - mirgenedb_hairpin = null - mirgenedb_gff = null - mirgenedb_species = null + genome = null + igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_ignore = false + mirna_gtf = null + mature = "https://mirbase.org/ftp/CURRENT/mature.fa.gz" + hairpin = "https://mirbase.org/ftp/CURRENT/hairpin.fa.gz" + mirgenedb = false + mirgenedb_mature = null + mirgenedb_hairpin = null + mirgenedb_gff = null + mirgenedb_species = null // Trimming options - clip_r1 = null - three_prime_clip_r1 = null - three_prime_adapter = null - trim_fastq = true - fastp_min_length = 17 - fastp_known_mirna_adapters = "$projectDir/assets/known_adapters.fa" - save_trimmed_fail = false - skip_qc = false - skip_fastqc = false - skip_multiqc = false - skip_mirdeep = false - skip_fastp = false - save_reference = false - fastp_max_length = 40 + clip_r1 = null + three_prime_clip_r1 = null + three_prime_adapter = null + trim_fastq = true + fastp_min_length = 17 + fastp_known_mirna_adapters = "$projectDir/assets/known_adapters.fa" + save_trimmed_fail = false + skip_qc = false + skip_fastqc = false + skip_multiqc = false + skip_mirdeep = false + skip_fastp = false + save_reference = false + fastp_max_length = 40 // Contamination filtering - filter_contamination = false - rrna = null - trna = null - cdna = null - ncrna = null - pirna = null - other_contamination = null + filter_contamination = false + rrna = null + trna = null + cdna = null + ncrna = null + pirna = null + other_contamination = null // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' + multiqc_config = null + multiqc_title = null + multiqc_logo = null + max_multiqc_email_size = '25.MB' multiqc_methods_description = null // Boilerplate options - outdir = null - tracedir = "${params.outdir}/pipeline_info" - publish_dir_mode = 'copy' - email = null - email_on_fail = null - plaintext_email = false - monochrome_logs = false - hook_url = null - help = false - validate_params = true - show_hidden_params = false - schema_ignore_params = 'genomes' - enable_conda = false + outdir = null + tracedir = "${params.outdir}/pipeline_info" + publish_dir_mode = 'copy' + email = null + email_on_fail = null + plaintext_email = false + monochrome_logs = false + hook_url = null + help = false + validate_params = true + show_hidden_params = false + schema_ignore_params = 'genomes' + enable_conda = false // Config options - custom_config_version = 'master' - custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" - config_profile_description = null - config_profile_contact = null - config_profile_url = null - config_profile_name = null + custom_config_version = 'master' + custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" + config_profile_description = null + config_profile_contact = null + config_profile_url = null + config_profile_name = null // Max resource options // Defaults only, expecting to be overwritten - max_memory = '128.GB' - max_cpus = 16 - max_time = '240.h' + max_memory = '128.GB' + max_cpus = 16 + max_time = '240.h' } @@ -112,64 +112,64 @@ try { profiles { debug { process.beforeScript = 'echo $HOSTNAME' } conda { - params.enable_conda = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + params.enable_conda = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } mamba { - params.enable_conda = true - conda.useMamba = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + params.enable_conda = true + conda.useMamba = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } docker { - docker.enabled = true - docker.userEmulation = true - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + docker.enabled = true + docker.userEmulation = true + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' } singularity { - singularity.enabled = true - singularity.autoMounts = true - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + singularity.enabled = true + singularity.autoMounts = true + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false } podman { - podman.enabled = true - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false + podman.enabled = true + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false } shifter { - shifter.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - charliecloud.enabled = false + shifter.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + charliecloud.enabled = false } charliecloud { - charliecloud.enabled = true - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false + charliecloud.enabled = true + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false } gitpod { - executor.name = 'local' - executor.cpus = 16 - executor.memory = 60.GB + executor.name = 'local' + executor.cpus = 16 + executor.memory = 60.GB } test { includeConfig 'conf/test.config' } test_no_genome { includeConfig 'conf/test_no_genome.config' } From bf3ef92df3bd77a90a44bc18f500021067c5e6fd Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Mon, 24 Oct 2022 22:20:47 +0000 Subject: [PATCH 3/3] Fix prettier --- docs/usage.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/docs/usage.md b/docs/usage.md index bc6c3a4b..28373e00 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -36,8 +36,6 @@ If MirGeneDB should be used instead it needs to be specified using `--mirgenedb` - `mirgenedb_mature`: points to the FASTA file of mature miRNA sequences. Download from `https://mirgenedb.org/download`. - `mirgenedb_hairpin`: points to the FASTA file of precursor miRNA sequences. Download from `https://mirgenedb.org/download`. Note that MirGeneDB does not have a dedicated `hairpin` file, but the `Precursor sequences` are to be used. - - ### Genome - `fasta`: the reference genome FASTA file