From a4dd908283ba651550da6891ac703890ef079e3d Mon Sep 17 00:00:00 2001 From: Aman Nalakath Date: Thu, 11 Dec 2025 14:40:29 +0100 Subject: [PATCH] using symlinks instead of f --- hello_world.nf | 74 +------------------------------------------------- test.nf | 0 wc-params.nf | 66 +------------------------------------------- word_count.nf | 71 +----------------------------------------------- 4 files changed, 3 insertions(+), 208 deletions(-) mode change 100644 => 120000 hello_world.nf create mode 100644 test.nf mode change 100644 => 120000 wc-params.nf mode change 100644 => 120000 word_count.nf diff --git a/hello_world.nf b/hello_world.nf deleted file mode 100644 index 70e94b4..0000000 --- a/hello_world.nf +++ /dev/null @@ -1,73 +0,0 @@ -// ch1 = Channel.value( 'GRCh38' ) -// ch2 = Channel.value( ['chr1', 'chr2', 'chr3', 'chr4', 'chr5'] ) -// ch3 = Channel.value( ['chr1' : 248956422, 'chr2' : 242193529, 'chr3' : 198295559] ) -// ch1.view() -// ch2.view() -// ch3.view() - - -// chromosome_ch = Channel.of(1..22, 'X', 'Y') -// chromosome_ch.view() - -// ch_vl = Channel.value('GRCh38') -// ch_qu = Channel.of(1..4) - -// ch_vl.view() -// ch_qu.view() - -// aligner_list = ['salmon', 'kallisto'] - -// aligner_ch = Channel.fromList(aligner_list) - -// aligner_ch.view() - -// ids = ['ERR908507', 'ERR908506', 'ERR908505'] - -// q_ids = Channel.fromList(ids) -// q_ids.view() - -// q_val = Channel.value(ids) -// q_val.view() - -// read_ch = Channel.fromPath( '../**.png', hidden: true ) -// read_ch.view() - -// read_ch = Channel.fromPath( 'data/chicken/reads/*.fq.gz', checkIfExists: true, hidden: true ) -// read_ch.view() - - -// -process.debug - - -// params.chr = "chr2" - -// process CHR_COUNT { - -// script: -// """ -// printf "Number of sequences for chromosome ${params.chr} :" -// grep -c '>'${params.chr} ${projectDir}/../Downloads/dm6.fa -// """ -// } - -// workflow { -// CHR_COUNT() -// } - -process NUM_IDS { - - script: - """ - #set bash variable NUMIDS - NUMIDS=`grep -c '^>' $params.transcriptome` - - echo 'Number of sequences' - printf "%'d\n" \$NUMIDS - """ -} - -params.transcriptome = "${projectDir}/../Downloads/dm6.fa" - -workflow { - NUM_IDS() -} \ No newline at end of file diff --git a/hello_world.nf b/hello_world.nf new file mode 120000 index 0000000..7ef7c5f --- /dev/null +++ b/hello_world.nf @@ -0,0 +1 @@ +/Users/aman/Documents/hello_world.nf \ No newline at end of file diff --git a/test.nf b/test.nf new file mode 100644 index 0000000..e69de29 diff --git a/wc-params.nf b/wc-params.nf deleted file mode 100644 index a4bca61..0000000 --- a/wc-params.nf +++ /dev/null @@ -1,65 +0,0 @@ -#!/usr/bin/env nextflow - - - -/* -======================================================================================== - Workflow parameters are written as params. - and can be initialised using the `=` operator. -======================================================================================== -*/ - -params.input = "data/yeast/reads/ref1_1.fq.gz" -params.sleep = 2 - -/* -======================================================================================== - Input data is received through channels -======================================================================================== -*/ - -input_ch = Channel.fromPath(params.input) - -/* -======================================================================================== - Main Workflow -======================================================================================== -*/ - -workflow { - // The script to execute is called by it's process name, and input is provided between brackets. - - NUM_LINES(input_ch) - - /* Process output is accessed using the `out` channel. - The channel operator view() is used to print process output to the terminal. */ - - NUM_LINES.out.view() - -} - -/* -======================================================================================== - A Nextflow process block. Process names are written, by convention, in uppercase. - This convention is used to enhance workflow readability. -======================================================================================== -*/ -process NUM_LINES { - - input: - path read - - output: - stdout - - script: - """ - sleep ${params.sleep} - - # Print file name - printf '${read}\\t' - - # Unzip file and count number of lines - gunzip -c ${read} | wc -l - """ -} \ No newline at end of file diff --git a/wc-params.nf b/wc-params.nf new file mode 120000 index 0000000..2e891b7 --- /dev/null +++ b/wc-params.nf @@ -0,0 +1 @@ +/Users/aman/Documents/wc-params.nf \ No newline at end of file diff --git a/word_count.nf b/word_count.nf deleted file mode 100644 index f3c7027..0000000 --- a/word_count.nf +++ /dev/null @@ -1,70 +0,0 @@ -#!/usr/bin/env nextflow - - - -/* -======================================================================================== - Workflow parameters are written as params. - and can be initialised using the `=` operator. -======================================================================================== -*/ - -params.input = "data/yeast/reads/ref1_1.fq.gz" - - -ch1 = Channel.value( 'GRCh38' ) -ch2 = Channel.value( ['chr1', 'chr2', 'chr3', 'chr4', 'chr5'] ) -ch3 = Channel.value( ['chr1' : 248956422, 'chr2' : 242193529, 'chr3' : 198295559] ) -ch1.view() -ch2.view() -ch3.view() - -/* -======================================================================================== - Input data is received through channels -======================================================================================== -*/ - -input_ch = Channel.fromPath(params.input) - -/* -======================================================================================== - Main Workflow -======================================================================================== -*/ - -workflow { - // The script to execute is called by it's process name, and input is provided between brackets. - - NUM_LINES(input_ch) - - /* Process output is accessed using the `out` channel. - The channel operator view() is used to print process output to the terminal. */ - - NUM_LINES.out.view() - -} - -/* -======================================================================================== - A Nextflow process block. Process names are written, by convention, in uppercase. - This convention is used to enhance workflow readability. -======================================================================================== -*/ -process NUM_LINES { - - input: - path read - - output: - stdout - - script: - """ - # Print file name - printf '${read}\\t' - - # Unzip file and count number of lines - gunzip -c ${read} | wc -l - """ -} \ No newline at end of file diff --git a/word_count.nf b/word_count.nf new file mode 120000 index 0000000..1af43f1 --- /dev/null +++ b/word_count.nf @@ -0,0 +1 @@ +/Users/aman/Documents/word_count.nf \ No newline at end of file