From 647c4e449eb4cc151f69525fba6919179d07a350 Mon Sep 17 00:00:00 2001
From: Aman Nalakath <aman.nalakath@tum.de>
Date: Tue, 9 Dec 2025 22:45:26 +0100
Subject: [PATCH] prj init

---
 README.md      |  0
 hello_world.nf | 73 ++++++++++++++++++++++++++++++++++++++++++++++++++
 wc-params.nf   | 65 ++++++++++++++++++++++++++++++++++++++++++++
 word_count.nf  | 70 +++++++++++++++++++++++++++++++++++++++++++++++
 4 files changed, 208 insertions(+)
 create mode 100644 README.md
 create mode 100644 hello_world.nf
 create mode 100644 wc-params.nf
 create mode 100644 word_count.nf

diff --git a/README.md b/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/hello_world.nf b/hello_world.nf
new file mode 100644
index 0000000..70e94b4
--- /dev/null
+++ b/hello_world.nf
@@ -0,0 +1,73 @@
+// 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/wc-params.nf b/wc-params.nf
new file mode 100644
index 0000000..a4bca61
--- /dev/null
+++ b/wc-params.nf
@@ -0,0 +1,65 @@
+#!/usr/bin/env nextflow
+
+
+
+/*
+========================================================================================
+    Workflow parameters are written as params.<parameter>
+    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/word_count.nf b/word_count.nf
new file mode 100644
index 0000000..f3c7027
--- /dev/null
+++ b/word_count.nf
@@ -0,0 +1,70 @@
+#!/usr/bin/env nextflow
+
+
+
+/*
+========================================================================================
+    Workflow parameters are written as params.<parameter>
+    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