From 14b02ee93d7a205771146ed51db9c17c29ee284d Mon Sep 17 00:00:00 2001
From: bfrgoncalves <bfgoncalves@medicina.ulisboa.pt>
Date: Mon, 24 Sep 2018 14:35:42 +0100
Subject: [PATCH 1/5] add flowcraft dockerfile

---
 docker/Dockerfile | 18 ++++++++++++++++++
 1 file changed, 18 insertions(+)
 create mode 100644 docker/Dockerfile

diff --git a/docker/Dockerfile b/docker/Dockerfile
new file mode 100644
index 00000000..dd73e6d4
--- /dev/null
+++ b/docker/Dockerfile
@@ -0,0 +1,18 @@
+FROM python:3.6-alpine3.7
+MAINTAINER Bruno Gonçalves <bfgoncalves@medicina.ulisboa.pt>
+
+RUN apk add --no-cache git
+
+WORKDIR /flowcraft
+
+# Clone FlowCraft
+RUN git clone https://github.com/assemblerflow/flowcraft.git
+WORKDIR ./flowcraft
+
+# Install flowcraft
+RUN python setup.py install
+
+WORKDIR /flowcraft
+
+# Remove unnecessary packages
+RUN apk del git
\ No newline at end of file

From be82be0893db00d3d4b44ad5ff4ff5542f15cdb2 Mon Sep 17 00:00:00 2001
From: Tiago Jesus <tiagofilipe12@gmail.com>
Date: Tue, 25 Sep 2018 15:39:25 +0100
Subject: [PATCH 2/5] updated docker images for mapping_patlas and mash_screen
 (#131)

* updated docker images for mapping_patlas and mash_screen

* updated changelog
---
 changelog.md                                          | 7 +++++++
 docs/user/components/mapping_patlas.rst               | 6 +++---
 docs/user/components/mash_dist.rst                    | 4 ++--
 docs/user/components/mash_screen.rst                  | 4 ++--
 flowcraft/generator/components/distance_estimation.py | 4 ++--
 flowcraft/generator/components/patlas_mapping.py      | 4 ++--
 flowcraft/generator/templates/mapping_patlas.nf       | 2 +-
 flowcraft/generator/templates/mash_dist.nf            | 2 +-
 8 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/changelog.md b/changelog.md
index a63add25..51ab253e 100644
--- a/changelog.md
+++ b/changelog.md
@@ -1,5 +1,12 @@
 # Changelog
 
+## Changes in upcoming release (dev branch) 
+
+### Components changes
+
+Updated images for components `mash_dist`, `mash_screen` and 
+`mapping_patlas`
+
 ## 1.3.0
 
 ### Features
diff --git a/docs/user/components/mapping_patlas.rst b/docs/user/components/mapping_patlas.rst
index 8488a15b..35327b3c 100644
--- a/docs/user/components/mapping_patlas.rst
+++ b/docs/user/components/mapping_patlas.rst
@@ -60,10 +60,10 @@ Default directives
 
 - ``mappingBowtie``:
     - ``container``: flowcraft/mapping-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``samtoolsView``:
     - ``container``: flowcraft/mapping-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``jsonDumpingMapping``:
     - ``container``: flowcraft/mapping-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
diff --git a/docs/user/components/mash_dist.rst b/docs/user/components/mash_dist.rst
index 7988163d..a47f4207 100644
--- a/docs/user/components/mash_dist.rst
+++ b/docs/user/components/mash_dist.rst
@@ -65,7 +65,7 @@ Default directives
 
 - ``runMashDist``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``mashDistOutputJson``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
diff --git a/docs/user/components/mash_screen.rst b/docs/user/components/mash_screen.rst
index 5d79f38b..c136aa89 100644
--- a/docs/user/components/mash_screen.rst
+++ b/docs/user/components/mash_screen.rst
@@ -60,7 +60,7 @@ Default directives
 
 - ``mashScreen``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
 - ``mashOutputJson``:
     - ``container``: flowcraft/mash-patlas
-    - ``version``: 1.4.1
+    - ``version``: 1.6.0-1
diff --git a/flowcraft/generator/components/distance_estimation.py b/flowcraft/generator/components/distance_estimation.py
index 1bc09de3..3db7bb41 100644
--- a/flowcraft/generator/components/distance_estimation.py
+++ b/flowcraft/generator/components/distance_estimation.py
@@ -43,13 +43,13 @@ def __init__(self, **kwargs):
         self.directives = {
             "runMashDist": {
                 "container": "flowcraft/mash-patlas",
-                "version": "1.5.2-1",
+                "version": "1.6.0-1",
                 "cpus": 1,
                 "memory": "{ 4.GB * task.attempt }"
             },
             "mashDistOutputJson": {
                 "container": "flowcraft/mash-patlas",
-                "version": "1.5.2-1",
+                "version": "1.6.0-1",
                 "cpus": 1,
                 "memory": "'4GB'"
             }
diff --git a/flowcraft/generator/components/patlas_mapping.py b/flowcraft/generator/components/patlas_mapping.py
index a3eca958..4bd68991 100644
--- a/flowcraft/generator/components/patlas_mapping.py
+++ b/flowcraft/generator/components/patlas_mapping.py
@@ -47,14 +47,14 @@ def __init__(self, **kwargs):
         self.directives = {
             "mappingBowtie": {
                 "container": "flowcraft/mapping-patlas",
-                "version": "1.5.2-2",
+                "version": "1.6.0-1",
                 "cpus": 1,
                 "memory": "{ 4.GB * task.attempt }",
                 "scratch": "true"
             },
             "jsonDumpingMapping": {
                 "container": "flowcraft/mapping-patlas",
-                "version": "1.5.2-2",
+                "version": "1.6.0-1",
                 "cpus": 1,
                 "memory": "'4GB'"
             }
diff --git a/flowcraft/generator/templates/mapping_patlas.nf b/flowcraft/generator/templates/mapping_patlas.nf
index 8643fcee..e4245c78 100644
--- a/flowcraft/generator/templates/mapping_patlas.nf
+++ b/flowcraft/generator/templates/mapping_patlas.nf
@@ -57,7 +57,7 @@ process jsonDumpingMapping_{{ pid }} {
 
     tag { sample_id }
 
-    publishDir 'results/mapping/mapping_json_{{ pid }}/', mode: 'copy'
+    publishDir 'results/mapping/mapping_json_{{ pid }}/'
 
     input:
     set sample_id, file(depthFile) from samtoolsResults
diff --git a/flowcraft/generator/templates/mash_dist.nf b/flowcraft/generator/templates/mash_dist.nf
index 13ae560f..50a46ff7 100644
--- a/flowcraft/generator/templates/mash_dist.nf
+++ b/flowcraft/generator/templates/mash_dist.nf
@@ -38,7 +38,7 @@ process mashDistOutputJson_{{ pid }} {
 
     tag { sample_id }
 
-    publishDir 'results/mashdist/mashdist_json_{{ pid }}/', mode: 'copy'
+    publishDir 'results/mashdist/mashdist_json_{{ pid }}/'
 
     input:
     set sample_id, fasta, file(mashtxt) from mashDistOutChannel_{{ pid }}

From a379785a79aff6e9b2464d552e160ef7337f2c51 Mon Sep 17 00:00:00 2001
From: Tiago Jesus <tiagofilipe12@gmail.com>
Date: Tue, 25 Sep 2018 15:48:38 +0100
Subject: [PATCH 3/5] added Fast ani component (#130)

* added fast ani component

* removed unused params

* fixed output name

* fixed input name

* fixed image tag

* added log to stderr

* added implementation of multi fasta parsing for fastani

* added channel for parameter fragLen

* added parser for main fasta

* changed docker img tag

* fixed file naming

* fixed pep8 issue

* added join to file name

* added documentation and publish dir

* updated changelog

* fixed file naming

* removed output_type

* fixed changelog
---
 changelog.md                                  |  6 ++-
 docs/user/available_components.rst            |  8 ++-
 docs/user/components/fast_ani.rst             | 47 ++++++++++++++++
 .../components/distance_estimation.py         | 29 ++++++++++
 flowcraft/generator/engine.py                 |  1 +
 flowcraft/generator/templates/fast_ani.nf     | 30 +++++++++++
 flowcraft/templates/fasta_spliter.py          | 53 +++++++++++++++++++
 7 files changed, 172 insertions(+), 2 deletions(-)
 create mode 100644 docs/user/components/fast_ani.rst
 create mode 100644 flowcraft/generator/templates/fast_ani.nf
 create mode 100755 flowcraft/templates/fasta_spliter.py

diff --git a/changelog.md b/changelog.md
index 51ab253e..c6a5066b 100644
--- a/changelog.md
+++ b/changelog.md
@@ -5,7 +5,11 @@
 ### Components changes
 
 Updated images for components `mash_dist`, `mash_screen` and 
-`mapping_patlas`
+`mapping_patlas`.
+
+### New components
+- Added component `fast_ani`.
+
 
 ## 1.3.0
 
diff --git a/docs/user/available_components.rst b/docs/user/available_components.rst
index 85034e62..d43e00d6 100644
--- a/docs/user/available_components.rst
+++ b/docs/user/available_components.rst
@@ -99,7 +99,13 @@ Distance Estimation
   plasmid database and generates a JSON input file for pATLAS. This component
   searches for containment of a given sequence in read sequencing data.
   However if a different database is provided it can use mash screen for other
-  purporses.
+  purposes.
+
+- :doc:`components/fast_ani`: Performs pairwise comparisons between fastas,
+given a multifasta as input for fastANI. It will split the multifasta into
+single fastas that will then be provided as a matrix. The output will be the
+all pairwise comparisons that pass the minimum of 50 aligned sequences with a
+default length of 200 bp.
 
 - :doc:`components/mash_sketch_fasta`: Performs mash sketch for fasta files.
 
diff --git a/docs/user/components/fast_ani.rst b/docs/user/components/fast_ani.rst
new file mode 100644
index 00000000..5c046d8c
--- /dev/null
+++ b/docs/user/components/fast_ani.rst
@@ -0,0 +1,47 @@
+fast_ani
+========
+
+Purpose
+-------
+
+This component performs pairwise comparisons between fastas,
+given a multifasta as input for fastANI. It will split the multifasta into
+single fastas that will then be provided as a matrix. The output will be the
+all pairwise comparisons that pass the minimum of 50 aligned sequences with a
+default length of 200 bp.
+
+Input/Output type
+------------------
+
+- Input type: ``fasta``
+- Output type: ``None``
+
+
+Parameters
+----------
+
+- ``fragLen``: Sets the minimum size of the fragment to be passed to
+`--fragLen` argument of fastANI.
+
+
+Published results
+-----------------
+
+- ``results/fast_ani/``: A text file with the extension `.out`, which has all
+the pairwise comparisons between sequences, reporting ANI.
+
+
+Published reports
+-----------------
+
+None.
+
+
+Default directives
+------------------
+
+- ``fastAniMatrix``:
+    - ``container``: flowcraft/fast_ani
+    - ``version``: 1.1.0-2
+    - ``cpus``: 20
+    - ``memory``: { 30.GB * task.attempt }
\ No newline at end of file
diff --git a/flowcraft/generator/components/distance_estimation.py b/flowcraft/generator/components/distance_estimation.py
index 3db7bb41..bed1bc0e 100644
--- a/flowcraft/generator/components/distance_estimation.py
+++ b/flowcraft/generator/components/distance_estimation.py
@@ -200,3 +200,32 @@ def __init__(self, **kwargs):
         self.status_channels = [
             "mashSketchFastq",
         ]
+
+
+class FastAniMatrix(Process):
+
+    def __init__(self, **kwargs):
+
+        super().__init__(**kwargs)
+
+        self.input_type = "fasta"
+
+        self.params = {
+            "fragLen": {
+                "default": 3000,
+                "description": "Set size of fragment. Default: 3000."
+            }
+        }
+
+        self.directives = {
+            "fastAniMatrix": {
+                "container": "flowcraft/fast_ani",
+                "version": "1.1.0-2",
+                "cpus": 20,
+                "memory": "{ 30.GB * task.attempt }"
+            },
+        }
+
+        self.status_channels = [
+            "fastAniMatrix",
+        ]
diff --git a/flowcraft/generator/engine.py b/flowcraft/generator/engine.py
index 4082ab69..cd238b1e 100644
--- a/flowcraft/generator/engine.py
+++ b/flowcraft/generator/engine.py
@@ -68,6 +68,7 @@
         "filter_poly": readsqc.FilterPoly,
         "integrity_coverage": readsqc.IntegrityCoverage,
         "fasterq_dump": downloads.FasterqDump,
+        "fast_ani": distest.FastAniMatrix,
         "kraken": meta.Kraken,
         "mafft": alignment.Mafft,
         "mapping_patlas": mapping_patlas.PatlasMapping,
diff --git a/flowcraft/generator/templates/fast_ani.nf b/flowcraft/generator/templates/fast_ani.nf
new file mode 100644
index 00000000..c052a2f4
--- /dev/null
+++ b/flowcraft/generator/templates/fast_ani.nf
@@ -0,0 +1,30 @@
+IN_fragLen_{{ pid }} = Channel.value(params.fragLen{{ param_id }})
+
+// runs fast ani for multiple comparisons (many to many mode)
+process fastAniMatrix_{{ pid }} {
+
+    {% include "post.txt" ignore missing %}
+
+    tag { sample_id }
+
+     publishDir 'results/fast_ani/fast_ani_{{ pid }}/',
+
+    input:
+    set sample_id, file(fasta) from {{ input_channel }}
+    val fragLenValue from IN_fragLen_{{ pid }}
+
+    output:
+    set sample_id, fasta, file("*.out")
+    {% with task_name="fastAniMatrix", sample_id="sample_id" %}
+    {%- include "compiler_channels.txt" ignore missing -%}
+    {% endwith %}
+
+    """
+    mkdir fasta_store
+    fasta_spliter.py ${fasta}
+    fastANI --ql files_fastani.txt --rl files_fastani.txt \
+    -t ${task.cpus} --fragLen ${fragLenValue} \
+    -o ${sample_id.take(sample_id.lastIndexOf("."))}_fastani.out
+    """
+
+}
diff --git a/flowcraft/templates/fasta_spliter.py b/flowcraft/templates/fasta_spliter.py
new file mode 100755
index 00000000..ff4227e6
--- /dev/null
+++ b/flowcraft/templates/fasta_spliter.py
@@ -0,0 +1,53 @@
+#!/usr/bin/env python3
+
+"""
+Purpose
+-------
+
+This module is intended to split all fastas in a multifasta file into different
+fasta files.
+
+Code documentation
+------------------
+
+"""
+
+import os
+import sys
+
+
+def main():
+
+    cwd = os.getcwd()
+    # a var to check if out_handle is started and if so it enables to control
+    # how it should be closed
+    out_handle = False
+    # opens the input file of the process
+    input_file = open(sys.argv[1])
+    # a file with the list of all paths to fasta files that will be used by
+    # fastANI
+    list_files = open("files_fastani.txt", "w")
+    # iterates by each entry in the fasta file
+    for line in input_file:
+        if line.startswith(">"):
+            if out_handle:
+                out_handle.close()
+            # writes the output to fasta store folder inside cwd, respective
+            # workdir
+            path_to_file = os.path.join(cwd, "fasta_store",
+                                        "_".join(line.split("_")[0:3])
+                                        .replace(">", "") + ".fas")
+            # writes to list of files
+            list_files.write(path_to_file + "\n")
+            out_handle = open(path_to_file, "w")
+            out_handle.write(line)
+        else:
+            out_handle.write(line)
+
+    out_handle.close()
+    input_file.close()
+    list_files.close()
+
+
+if __name__ == "__main__":
+    main()

From 10633e92573ff5cb34728f37a6588f0243aede2f Mon Sep 17 00:00:00 2001
From: odiogosilva <o.diogosilva@gmail.com>
Date: Wed, 26 Sep 2018 11:21:02 +0100
Subject: [PATCH 4/5] Added `--export-directives` option to `build` mode to
 export component's directives in JSON format to standard output.

---
 changelog.md                  |  6 +++++-
 flowcraft/flowcraft.py        | 16 +++++++++++++---
 flowcraft/generator/engine.py | 13 +++++++++++++
 3 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/changelog.md b/changelog.md
index c6a5066b..2890f7aa 100644
--- a/changelog.md
+++ b/changelog.md
@@ -1,6 +1,6 @@
 # Changelog
 
-## Changes in upcoming release (dev branch) 
+## Changes in upcoming release (`dev` branch) 
 
 ### Components changes
 
@@ -10,6 +10,10 @@ Updated images for components `mash_dist`, `mash_screen` and
 ### New components
 - Added component `fast_ani`.
 
+### Minor/Other changes
+
+- Added `--export-directives` option to `build` mode to export component's 
+directives in JSON format to standard output.
 
 ## 1.3.0
 
diff --git a/flowcraft/flowcraft.py b/flowcraft/flowcraft.py
index 32745e0f..fea5c2d9 100755
--- a/flowcraft/flowcraft.py
+++ b/flowcraft/flowcraft.py
@@ -97,6 +97,12 @@ def get_args(args=None):
                          "components (via -t option) in JSON format to stdout. "
                          "No pipeline will be generated with this option."
     )
+    build_parser.add_argument(
+        "--export-directives", dest="export_directives", action="store_const",
+        const=True, help="Only export the directives for the provided "
+                         "components (via -t option) in JSON format to stdout. "
+                         "No pipeline will be generated with this option."
+    )
 
     # GENERAL OPTIONS
     parser.add_argument(
@@ -177,7 +183,7 @@ def validate_build_arguments(args):
 
     # Skill all checks when exporting parameters AND providing at least one
     # component
-    if args.export_params:
+    if args.export_params or args.export_directives:
         # Check if components provided
         if not args.tasks:
             logger.error(colored_print(
@@ -266,8 +272,9 @@ def copy_project(path):
 
 def build(args):
 
-    # Disable standard logging for stdout when the following modes are executed:
-    if args.export_params:
+    # Disable standard logging for stdout when the following modes are
+    #  executed:
+    if args.export_params or args.export_directives:
         logger.setLevel(logging.ERROR)
 
     welcome = [
@@ -330,6 +337,9 @@ def build(args):
     if args.export_params:
         nfg.export_params()
         sys.exit(0)
+    elif args.export_directives:
+        nfg.export_directives()
+        sys.exit(0)
     else:
         # building the actual pipeline nf file
         nfg.build()
diff --git a/flowcraft/generator/engine.py b/flowcraft/generator/engine.py
index cd238b1e..f4083f3d 100644
--- a/flowcraft/generator/engine.py
+++ b/flowcraft/generator/engine.py
@@ -1506,6 +1506,19 @@ def export_params(self):
         # Flush params json to stdout
         sys.stdout.write(json.dumps(params_json))
 
+    def export_directives(self):
+        """Export pipeline directives as a JSON to stdout
+        """
+
+        directives_json = {}
+
+        # Skip first init process
+        for p in self.processes[1:]:
+            directives_json[p.template] = p.directives
+
+        # Flush params json to stdout
+        sys.stdout.write(json.dumps(directives_json))
+
     def build(self):
         """Main pipeline builder
 

From 07083f26d07635dc9733e8ad97ea22ddce856bc7 Mon Sep 17 00:00:00 2001
From: Diogo Silva <o.diogosilva@gmail.com>
Date: Thu, 27 Sep 2018 15:24:30 +0100
Subject: [PATCH 5/5] Clear checkpoint (#132)

* Added comments

* Started implementing component specific input clear

* Finished implementing component specific input clear

* Added condition to remove input only after successful execution

* Added more date information in `inspect` mode, including the year and the
locale of the executing system.

* Added changelog entry
---
 changelog.md                                  | 10 ++++-
 flowcraft/generator/components/assembly.py    | 35 ++++++++++++++--
 .../components/assembly_processing.py         | 11 +++++
 flowcraft/generator/components/mapping.py     | 20 ++++++++-
 .../generator/components/metagenomics.py      | 33 +++++++++++++++
 .../components/reads_quality_control.py       | 41 +++++++++++++++++--
 flowcraft/generator/components/typing.py      | 11 +++++
 flowcraft/generator/inspect.py                | 13 +++++-
 flowcraft/generator/templates/bowtie.nf       | 20 ++++++++-
 .../generator/templates/downsample_fastq.nf   |  2 +-
 .../generator/templates/fastqc_trimmomatic.nf |  2 +-
 flowcraft/generator/templates/filter_poly.nf  | 19 ++++++++-
 flowcraft/generator/templates/maxbin2.nf      | 23 ++++++++++-
 flowcraft/generator/templates/megahit.nf      |  3 ++
 flowcraft/generator/templates/metaspades.nf   |  3 ++
 flowcraft/generator/templates/momps.nf        | 15 +++++++
 flowcraft/generator/templates/pilon.nf        | 15 +++++++
 .../generator/templates/reads_download.nf     |  6 ++-
 flowcraft/generator/templates/remove_host.nf  | 33 +++++++++++----
 flowcraft/generator/templates/skesa.nf        |  2 +-
 flowcraft/generator/templates/spades.nf       |  2 +-
 flowcraft/generator/templates/trimmomatic.nf  |  2 +-
 .../generator/templates/viral_assembly.nf     |  8 ++--
 flowcraft/templates/megahit.py                | 33 ++++++++++++++-
 flowcraft/templates/metaspades.py             | 31 +++++++++++++-
 flowcraft/templates/spades.py                 |  2 +-
 flowcraft/templates/trimmomatic.py            |  4 +-
 27 files changed, 361 insertions(+), 38 deletions(-)

diff --git a/changelog.md b/changelog.md
index 2890f7aa..d42e985c 100644
--- a/changelog.md
+++ b/changelog.md
@@ -2,9 +2,15 @@
 
 ## Changes in upcoming release (`dev` branch) 
 
+### Features
+
+- Added a new `clearInput` parameter to components that change their input.
+The aim of this option is to allow the controlled removal of temporary files,
+which is particularly useful in very large workflows.
+
 ### Components changes
 
-Updated images for components `mash_dist`, `mash_screen` and 
+- Updated images for components `mash_dist`, `mash_screen` and 
 `mapping_patlas`.
 
 ### New components
@@ -14,6 +20,8 @@ Updated images for components `mash_dist`, `mash_screen` and
 
 - Added `--export-directives` option to `build` mode to export component's 
 directives in JSON format to standard output.
+- Added more date information in `inspect` mode, including the year and the
+locale of the executing system.
 
 ## 1.3.0
 
diff --git a/flowcraft/generator/components/assembly.py b/flowcraft/generator/components/assembly.py
index 72749ee8..d6d8f8d4 100644
--- a/flowcraft/generator/components/assembly.py
+++ b/flowcraft/generator/components/assembly.py
@@ -50,6 +50,14 @@ def __init__(self, **kwargs):
                     "If 'auto' the SPAdes k-mer lengths will be determined "
                     "from the maximum read length of each assembly. If "
                     "'default', SPAdes will use the default k-mer lengths. "
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
@@ -81,6 +89,18 @@ def __init__(self, **kwargs):
             "scratch": "true"
         }}
 
+        self.params = {
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
+            }
+        }
+
+
 class ViralAssembly(Process):
     """
     Process to assemble viral genomes, based on SPAdes and megahit
@@ -95,7 +115,8 @@ def __init__(self, **kwargs):
 
         self.dependencies = ["integrity_coverage"]
 
-        self.status_channels = ["va_spades" , "va_megahit", "report_viral_assembly"]
+        self.status_channels = ["va_spades", "va_megahit",
+                                "report_viral_assembly"]
 
         self.link_end.append({"link": "SIDE_max_len", "alias": "SIDE_max_len"})
 
@@ -105,7 +126,7 @@ def __init__(self, **kwargs):
             "container": "flowcraft/viral_assembly",
             "version": "0.1-1",
             "scratch": "true"
-        },"va_megahit": {
+        }, "va_megahit": {
             "cpus": 4,
             "memory": "{ 5.GB * task.attempt }",
             "container": "flowcraft/viral_assembly",
@@ -146,5 +167,13 @@ def __init__(self, **kwargs):
                     "from the maximum read length of each assembly. If "
                     "'default', megahit will use the default k-mer lengths. "
                     "(default: $params.megahitKmers)"
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
-        }
\ No newline at end of file
+        }
diff --git a/flowcraft/generator/components/assembly_processing.py b/flowcraft/generator/components/assembly_processing.py
index 549ec74b..288ba61a 100644
--- a/flowcraft/generator/components/assembly_processing.py
+++ b/flowcraft/generator/components/assembly_processing.py
@@ -204,6 +204,17 @@ def __init__(self, **kwargs):
         self.link_end.append({"link": "SIDE_BpCoverage",
                               "alias": "SIDE_BpCoverage"})
 
+        self.params = {
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
+            }
+        }
+
         self.directives = {
             "pilon": {
                 "cpus": 4,
diff --git a/flowcraft/generator/components/mapping.py b/flowcraft/generator/components/mapping.py
index 53c3577f..a50b6403 100644
--- a/flowcraft/generator/components/mapping.py
+++ b/flowcraft/generator/components/mapping.py
@@ -32,6 +32,14 @@ def __init__(self, **kwargs):
                 "default": "null",
                 "description": "Specifies the reference indexes to be provided "
                                "to bowtie2."
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
@@ -55,8 +63,10 @@ def __init__(self, **kwargs):
             "report_bowtie"
         ]
 
+
 class Retrieve_mapped(Process):
-    """Samtools process to  to align short paired-end sequencing reads to long reference sequences
+    """Samtools process to  to align short paired-end sequencing reads to
+    long reference sequences
 
         This process is set with:
 
@@ -74,6 +84,14 @@ def __init__(self, **kwargs):
         self.output_type = "fastq"
 
         self.params = {
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
+            }
         }
 
         self.dependencies = ["bowtie"]
diff --git a/flowcraft/generator/components/metagenomics.py b/flowcraft/generator/components/metagenomics.py
index 07102fe5..3fcaf3d7 100644
--- a/flowcraft/generator/components/metagenomics.py
+++ b/flowcraft/generator/components/metagenomics.py
@@ -4,6 +4,7 @@
 except ImportError:
     from flowcraft.generator.process import Process
 
+
 class Kraken(Process):
     """kraken process template interface
 
@@ -80,6 +81,14 @@ def __init__(self, **kwargs):
                 "default": 0.9,
                 "description": "probability threshold for EM final classification."
                                "Default: 0.9"
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
@@ -129,6 +138,14 @@ def __init__(self, **kwargs):
                     "from the maximum read length of each assembly. If "
                     "'default', megahit will use the default k-mer lengths. "
                     "(default: $params.megahitKmers)"
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
@@ -173,6 +190,14 @@ def __init__(self, **kwargs):
                     "from the maximum read length of each assembly. If "
                     "'default', metaSPAdes will use the default k-mer lengths. "
                     "(default: $params.metaspadesKmers)"
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
@@ -245,6 +270,14 @@ def __init__(self, **kwargs):
                 "default": "'/index_hg19/hg19'",
                 "description": "Specifies the reference indexes to be provided "
                                "to bowtie2."
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
diff --git a/flowcraft/generator/components/reads_quality_control.py b/flowcraft/generator/components/reads_quality_control.py
index f130d4cf..6a7d52b0 100644
--- a/flowcraft/generator/components/reads_quality_control.py
+++ b/flowcraft/generator/components/reads_quality_control.py
@@ -215,6 +215,14 @@ def __init__(self, **kwargs):
                 "default": "55",
                 "description":
                     "Drop the read if it is below a specified length "
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
@@ -292,6 +300,14 @@ def __init__(self, **kwargs):
                 "default": "55",
                 "description":
                     "Drop the read if it is below a specified length."
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
@@ -334,9 +350,18 @@ def __init__(self, **kwargs):
                 "default": "'A 50%; T 50%; N 50%'",
                 "description":
                     "Pattern to filter the reads. Please separate parameter"
-                    "values with a space and separate new parameter sets with semicolon (;)."
-                    "Parameters are defined by two values: the pattern (any combination of the"
-                    "letters ATCGN), and the number of repeats or percentage of occurence."
+                    "values with a space and separate new parameter sets with"
+                    " semicolon (;). Parameters are defined by two values: "
+                    "the pattern (any combination of the letters ATCGN), and "
+                    "the number of repeats or percentage of occurence."
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
@@ -381,6 +406,14 @@ def __init__(self, **kwargs):
                 "description":
                     "Maximum estimated depth coverage allowed. FastQ with "
                     "higher estimated depth will be subsampled to this value."
+            },
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
             }
         }
 
@@ -393,4 +426,4 @@ def __init__(self, **kwargs):
 
         self.status_channels = [
             "downsample_fastq"
-        ]
\ No newline at end of file
+        ]
diff --git a/flowcraft/generator/components/typing.py b/flowcraft/generator/components/typing.py
index 5b7932cd..e0c3c255 100644
--- a/flowcraft/generator/components/typing.py
+++ b/flowcraft/generator/components/typing.py
@@ -106,6 +106,17 @@ def __init__(self, **kwargs):
 
         self.link_end.append({"link": "__fastq", "alias": "_LAST_fastq"})
 
+        self.params = {
+            "clearInput": {
+                "default": "false",
+                "description":
+                    "Permanently removes temporary input files. This option "
+                    "is only useful to remove temporary files in large "
+                    "workflows and prevents nextflow's resume functionality. "
+                    "Use with caution."
+            }
+        }
+
         self.directives = {
             "momps": {
                 "cpus": 3,
diff --git a/flowcraft/generator/inspect.py b/flowcraft/generator/inspect.py
index f5d6ea4f..af049f44 100644
--- a/flowcraft/generator/inspect.py
+++ b/flowcraft/generator/inspect.py
@@ -1,6 +1,7 @@
 import re
 import os
 import sys
+import time
 import curses
 import signal
 import locale
@@ -1378,6 +1379,13 @@ def _send_status_info(self, run_id):
         general_details = self._prepare_general_details()
         status_data = self._prepare_run_status_data()
 
+        # Add current year to start and stop dates
+        time_start = "{} {}".format(time.strftime("%Y"), self.time_start)
+        time_stop = "{} {}".format(time.strftime("%Y"), self.time_stop) \
+            if self.time_stop else "-"
+        # Get enconding for proper parsing of time
+        time_locale = locale.getlocale()[0]
+
         status_json = {
             "generalOverview": overview_data,
             "generalDetails": general_details,
@@ -1386,8 +1394,9 @@ def _send_status_info(self, run_id):
             "processInfo": self._convert_process_dict(),
             "processTags": self.process_tags,
             "runStatus": status_data,
-            "timeStart": str(self.time_start),
-            "timeStop": str(self.time_stop) if self.time_stop else "-",
+            "timeStart": time_start,
+            "timeStop": time_stop,
+            "timeLocale": time_locale,
             "processes": list(self.processes)
         }
 
diff --git a/flowcraft/generator/templates/bowtie.nf b/flowcraft/generator/templates/bowtie.nf
index 7c9526b8..fda6c5b8 100644
--- a/flowcraft/generator/templates/bowtie.nf
+++ b/flowcraft/generator/templates/bowtie.nf
@@ -5,6 +5,8 @@ if (params.index{{ param_id }} == null && params.reference{{ param_id }} == null
     exit 1, "Provide only an index OR a reference fasta file."
 }
 
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
 
 if (params.reference{{ param_id }}){
 
@@ -61,7 +63,23 @@ process bowtie_{{ pid }} {
 
     script:
     """
-    bowtie2 -x $index -1 ${fastq_pair[0]} -2 ${fastq_pair[1]} -p $task.cpus 1> ${sample_id}.bam 2> ${sample_id}_bowtie2.log
+    {
+        bowtie2 -x $index -1 ${fastq_pair[0]} -2 ${fastq_pair[1]} -p $task.cpus 1> ${sample_id}.bam 2> ${sample_id}_bowtie2.log
+
+        if [ "$clear" = "true" ];
+        then
+            work_regex=".*/work/.{2}/.{30}/.*"
+            file_source1=\$(readlink -f \$(pwd)/${fastq_pair[0]})
+            file_source2=\$(readlink -f \$(pwd)/${fastq_pair[1]})
+            if [[ "\$file_source1" =~ \$work_regex ]]; then
+                rm \$file_source1 \$file_source2
+            fi
+        fi
+
+        echo pass > .status
+    } || {
+        echo fail > .status
+    }
     """
 }
 
diff --git a/flowcraft/generator/templates/downsample_fastq.nf b/flowcraft/generator/templates/downsample_fastq.nf
index 942886e5..4beea248 100644
--- a/flowcraft/generator/templates/downsample_fastq.nf
+++ b/flowcraft/generator/templates/downsample_fastq.nf
@@ -5,7 +5,7 @@ IN_genome_size_{{ pid }} = Channel.value(params.genomeSize{{ param_id }})
 IN_depth_{{ pid }} = Channel.value(params.depth{{ param_id }})
     .map{it -> it.toString().isNumber() ? it : exit(1, "The depth parameter must be a number or a float. Provided value: '${params.depth{{ param_id }}}'")}
 
-clear = params.clearAtCheckpoint ? "true" : "false"
+clear = params.clearInput{{ param_id }} ? "true" : "false"
 checkpointClear_{{ pid }} = Channel.value(clear)
 
 process downsample_fastq_{{ pid }} {
diff --git a/flowcraft/generator/templates/fastqc_trimmomatic.nf b/flowcraft/generator/templates/fastqc_trimmomatic.nf
index 1bd182d7..8e78282d 100644
--- a/flowcraft/generator/templates/fastqc_trimmomatic.nf
+++ b/flowcraft/generator/templates/fastqc_trimmomatic.nf
@@ -15,7 +15,7 @@ if ( !params.trimMinLength{{ param_id }}.toString().isNumber() ){
 IN_trimmomatic_opts_{{ pid }} = Channel.value([params.trimSlidingWindow{{ param_id }},params.trimLeading{{ param_id }},params.trimTrailing{{ param_id }},params.trimMinLength{{ param_id }}])
 IN_adapters_{{ pid }} = Channel.value(params.adapters{{ param_id }})
 
-clear = params.clearAtCheckpoint ? "true" : "false"
+clear = params.clearInput{{ param_id }} ? "true" : "false"
 checkpointClear_{{ pid }} = Channel.value(clear)
 
 process fastqc_{{ pid }} {
diff --git a/flowcraft/generator/templates/filter_poly.nf b/flowcraft/generator/templates/filter_poly.nf
index 9f45d8a9..8477c61d 100644
--- a/flowcraft/generator/templates/filter_poly.nf
+++ b/flowcraft/generator/templates/filter_poly.nf
@@ -1,5 +1,7 @@
 IN_adapter_{{ pid }} = Channel.value(params.adapter{{ param_id }})
 
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
 
 process filter_poly_{{ pid }} {
 
@@ -7,12 +9,14 @@ process filter_poly_{{ pid }} {
     {% include "post.txt" ignore missing %}
 
     tag { sample_id }
+    echo true
 
     errorStrategy { task.exitStatus == 120 ? 'ignore' : 'retry' }
 
     input:
     set sample_id, file(fastq_pair) from {{ input_channel }}
     val adapter from IN_adapter_{{ pid }}
+    val clear from checkpointClear_{{ pid }}
 
     output:
     set sample_id , file("${sample_id}_filtered_{1,2}.fastq.gz") into {{ output_channel }}
@@ -32,12 +36,25 @@ process filter_poly_{{ pid }} {
     fi
     done
 
-    prinseq-lite.pl --fastq ${sample_id}_1.fq  --fastq2 ${sample_id}_2.fq  --custom_params "${adapter}" -out_format 3 -out_good ${sample_id}_filtered
+    #prinseq-lite.pl --fastq ${sample_id}_1.fq  --fastq2 ${sample_id}_2.fq  --custom_params "${adapter}" -out_format 3 -out_good ${sample_id}_filtered
+    touch ${sample_id}_filtered_1.fastq
+    touch ${sample_id}_filtered_2.fastq
+    touch "somerhin.fastq"
 
     gzip ${sample_id}_filtered_*.fastq
 
     rm *.fq *.fastq
 
+    if [ "$clear" = "true" ];
+    then
+        work_regex=".*/work/.{2}/.{30}/.*"
+        file_source1=\$(readlink -f \$(pwd)/${fastq_pair[0]})
+        file_source2=\$(readlink -f \$(pwd)/${fastq_pair[1]})
+        if [[ "\$file_source1" =~ \$work_regex ]]; then
+            rm \$file_source1 \$file_source2
+        fi
+    fi
+
     """
 }
 
diff --git a/flowcraft/generator/templates/maxbin2.nf b/flowcraft/generator/templates/maxbin2.nf
index 692300dc..5bce7100 100644
--- a/flowcraft/generator/templates/maxbin2.nf
+++ b/flowcraft/generator/templates/maxbin2.nf
@@ -2,6 +2,9 @@ IN_min_contig_lenght_{{ pid }} = Channel.value(params.min_contig_lenght{{ param_
 IN_max_iteration_{{ pid }} = Channel.value(params.max_iteration{{ param_id }})
 IN_prob_threshold_{{ pid }} = Channel.value(params.prob_threshold{{ param_id }})
 
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
+
 process maxbin2_{{ pid }} {
 
     // Send POST request to platform
@@ -16,7 +19,7 @@ process maxbin2_{{ pid }} {
     val minContigLenght from IN_min_contig_lenght_{{ pid }}
     val maxIterations from IN_max_iteration_{{ pid }}
     val probThreshold from IN_prob_threshold_{{ pid }}
-
+    val clear from checkpointClear_{{ pid }}
 
     output:
     file '*_maxbin.*.fasta' into binCh_{{ pid }}
@@ -27,7 +30,23 @@ process maxbin2_{{ pid }} {
 
     script:
     """
-    run_MaxBin.pl -contig ${assembly} -out ${sample_id}_maxbin -reads ${fastq[0]} -reads2 ${fastq[1]} -thread $task.cpus -min_contig_length ${minContigLenght} -max_iteration ${maxIterations} -prob_threshold ${probThreshold}
+    {
+        run_MaxBin.pl -contig ${assembly} -out ${sample_id}_maxbin -reads ${fastq[0]} -reads2 ${fastq[1]} -thread $task.cpus -min_contig_length ${minContigLenght} -max_iteration ${maxIterations} -prob_threshold ${probThreshold}
+        echo pass > .status
+
+        if [ "$clear" = "true" ];
+        then
+            work_regex=".*/work/.{2}/.{30}/.*"
+            file_source1=\$(readlink -f \$(pwd)/${fastq[0]})
+            file_source2=\$(readlink -f \$(pwd)/${fastq[1]})
+            assembly_file=\$(readlink -f \$(pwd)/${assembly})
+            if [[ "\$file_source1" =~ \$work_regex ]]; then
+                rm \$file_source1 \$file_source2 \$assembly_file
+            fi
+        fi
+    } || {
+        echo fail > .status
+    }
     """
 }
 
diff --git a/flowcraft/generator/templates/megahit.nf b/flowcraft/generator/templates/megahit.nf
index bc8f8165..8a5d7a7d 100644
--- a/flowcraft/generator/templates/megahit.nf
+++ b/flowcraft/generator/templates/megahit.nf
@@ -5,6 +5,8 @@ if ( params.megahitKmers{{ param_id }}.toString().split(" ").size() <= 1 ){
 }
 IN_megahit_kmers_{{ pid }} = Channel.value(params.megahitKmers{{ param_id }})
 
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
 
 process megahit_{{ pid }} {
 
@@ -17,6 +19,7 @@ process megahit_{{ pid }} {
     input:
     set sample_id, file(fastq_pair), max_len from {{ input_channel }}.join(SIDE_max_len_{{ pid }})
     val kmers from IN_megahit_kmers_{{ pid }}
+    val clear from checkpointClear_{{ pid }}
 
     output:
     set sample_id, file('*megahit*.fasta') into {{ output_channel }}
diff --git a/flowcraft/generator/templates/metaspades.nf b/flowcraft/generator/templates/metaspades.nf
index d7ce717c..685eb109 100644
--- a/flowcraft/generator/templates/metaspades.nf
+++ b/flowcraft/generator/templates/metaspades.nf
@@ -5,6 +5,8 @@ if ( params.metaspadesKmers{{ param_id }}.toString().split(" ").size() <= 1 ){
 }
 IN_metaspades_kmers_{{pid}} = Channel.value(params.metaspadesKmers{{ param_id }})
 
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
 
 process metaspades_{{ pid }} {
 
@@ -17,6 +19,7 @@ process metaspades_{{ pid }} {
     input:
     set sample_id, file(fastq_pair), max_len from {{ input_channel }}.join(SIDE_max_len_{{ pid }})
     val kmers from IN_metaspades_kmers_{{pid}}
+    val clear from checkpointClear_{{ pid }}
 
     output:
     set sample_id, file('*_metaspades*.fasta') into {{ output_channel }}
diff --git a/flowcraft/generator/templates/momps.nf b/flowcraft/generator/templates/momps.nf
index c1ea55ba..aad23e22 100644
--- a/flowcraft/generator/templates/momps.nf
+++ b/flowcraft/generator/templates/momps.nf
@@ -1,4 +1,7 @@
 
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
+
 process momps_{{ pid }} {
 
     // Send POST request to platform
@@ -8,6 +11,7 @@ process momps_{{ pid }} {
 
     input:
     set sample_id, file(assembly), file(fastq) from {{ input_channel }}.join(_LAST_fastq_{{ pid }})
+    val clear from checkpointClear_{{ pid }}
 
     output:
     file("*_st.tsv") into momps_st_{{ pid }}
@@ -39,6 +43,17 @@ process momps_{{ pid }} {
             # Get the profile for the sample
             echo $sample_id\t\$(awk "NR == 7" res/*.MLST_res.txt) > ${sample_id}_profile.tsv
             rm -r res
+
+            # Remove temporary input files when the clearInput option is used
+            if [ "$clear" = "true" ];
+            then
+                work_regex=".*/work/.{2}/.{30}/.*"
+                file_source1=\$(readlink -f \$(pwd)/${fastq_pair[0]})
+                file_source2=\$(readlink -f \$(pwd)/${fastq_pair[1]})
+                if [[ "\$file_source1" =~ \$work_regex ]]; then
+                    rm \$file_source1 \$file_source2
+                fi
+            fi
         else
             echo fail > .status
             rm -r res
diff --git a/flowcraft/generator/templates/pilon.nf b/flowcraft/generator/templates/pilon.nf
index 6a59c0e6..f85f577d 100644
--- a/flowcraft/generator/templates/pilon.nf
+++ b/flowcraft/generator/templates/pilon.nf
@@ -1,4 +1,7 @@
 
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
+
 process pilon_{{ pid }} {
 
     // Send POST request to platform
@@ -10,6 +13,7 @@ process pilon_{{ pid }} {
 
     input:
     set sample_id, file(assembly), file(bam_file), file(bam_index) from {{ input_channel }}
+    val clear from checkpointClear_{{ pid }}
 
     output:
     set sample_id, '*_polished.fasta' into {{ output_channel }}, pilon_report_{{ pid }}
@@ -23,6 +27,17 @@ process pilon_{{ pid }} {
         pilon_mem=${String.valueOf(task.memory).substring(0, String.valueOf(task.memory).length() - 1).replaceAll("\\s", "")}
         java -jar -Xms256m -Xmx\${pilon_mem} /NGStools/pilon-1.22.jar --genome $assembly --frags $bam_file --output ${assembly.name.replaceFirst(~/\.[^\.]+$/, '')}_polished --changes --threads $task.cpus >> .command.log 2>&1
         echo pass > .status
+
+        if [ "$clear" = "true" ];
+        then
+            work_regex=".*/work/.{2}/.{30}/.*"
+            assembly_file=\$(readlink -f \$(pwd)/${assembly})
+            bam_file=\$(readlink -f \$(pwd)/${bam_file})
+            if [[ "\$assembly_file" =~ \$work_regex ]]; then
+                rm \$assembly_file \$bam_file
+            fi
+        fi
+
     } || {
         echo fail > .status
     }
diff --git a/flowcraft/generator/templates/reads_download.nf b/flowcraft/generator/templates/reads_download.nf
index 9292cffa..3b77985d 100644
--- a/flowcraft/generator/templates/reads_download.nf
+++ b/flowcraft/generator/templates/reads_download.nf
@@ -17,7 +17,7 @@ process reads_download_{{ pid }} {
     maxRetries 1
 
     input:
-     set val(accession_id), val(name) from reads_download_in_1_0.splitText(){ it.trim() }.filter{ it != "" }.map{ it.split().length > 1 ? ["accession": it.split()[0], "name": it.split()[1]] : [it.split()[0], null] }
+    set val(accession_id), val(name) from reads_download_in_1_0.splitText(){ it.trim() }.filter{ it != "" }.map{ it.split().length > 1 ? ["accession": it.split()[0], "name": it.split()[1]] : [it.split()[0], null] }
     each file(aspera_key) from IN_asperaKey_{{ pid }}
 
     output:
@@ -29,7 +29,9 @@ process reads_download_{{ pid }} {
     script:
     """
     {
+        # getSeqENA requires accession numbers to be provided as a text file
         echo "${accession_id}" >> accession_file.txt
+        # Set default status value. It will be overwritten if anything goes wrong
         echo "pass" > ".status"
 
         if [ -f $aspera_key ]; then
@@ -40,6 +42,8 @@ process reads_download_{{ pid }} {
 
         getSeqENA.py -l accession_file.txt \$asperaOpt -o ./ --SRAopt --downloadCramBam
 
+        # If a name has been provided along with the accession, rename the
+        # fastq files.
         if [ $name != null ];
         then
             echo renaming pattern '${accession_id}' to '${name}' && cd ${accession_id} && rename "s/${accession_id}/${name}/" *.gz
diff --git a/flowcraft/generator/templates/remove_host.nf b/flowcraft/generator/templates/remove_host.nf
index aee89c84..f070c546 100644
--- a/flowcraft/generator/templates/remove_host.nf
+++ b/flowcraft/generator/templates/remove_host.nf
@@ -1,5 +1,7 @@
 IN_index_files_{{ pid }} = Channel.value(params.refIndex{{ param_id }})
 
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClear_{{ pid }} = Channel.value(clear)
 
 process remove_host_{{ pid }} {
 
@@ -12,6 +14,7 @@ process remove_host_{{ pid }} {
     input:
     set sample_id, file(fastq_pair) from {{ input_channel }}
     val bowtie2Index from IN_index_files_{{ pid }}
+    val clear from checkpointClear_{{ pid }}
 
     output:
     set sample_id , file("${sample_id}*.headersRenamed_*.fq.gz") into {{ output_channel }}
@@ -22,21 +25,35 @@ process remove_host_{{ pid }} {
 
     script:
     """
-    bowtie2 -x ${bowtie2Index} -1 ${fastq_pair[0]} -2 ${fastq_pair[1]} -p $task.cpus 1> ${sample_id}.bam 2> ${sample_id}_bowtie2.log
+    {
+        bowtie2 -x ${bowtie2Index} -1 ${fastq_pair[0]} -2 ${fastq_pair[1]} -p $task.cpus 1> ${sample_id}.bam 2> ${sample_id}_bowtie2.log
 
-    samtools view -buh -f 12 -o ${sample_id}_samtools.bam -@ $task.cpus ${sample_id}.bam
+        samtools view -buh -f 12 -o ${sample_id}_samtools.bam -@ $task.cpus ${sample_id}.bam
 
-    rm ${sample_id}.bam
+        rm ${sample_id}.bam
 
-    samtools fastq -1 ${sample_id}_unmapped_1.fq -2 ${sample_id}_unmapped_2.fq ${sample_id}_samtools.bam
+        samtools fastq -1 ${sample_id}_unmapped_1.fq -2 ${sample_id}_unmapped_2.fq ${sample_id}_samtools.bam
 
-    rm ${sample_id}_samtools.bam
+        rm ${sample_id}_samtools.bam
 
-    renamePE_samtoolsFASTQ.py -1 ${sample_id}_unmapped_1.fq -2 ${sample_id}_unmapped_2.fq
+        renamePE_samtoolsFASTQ.py -1 ${sample_id}_unmapped_1.fq -2 ${sample_id}_unmapped_2.fq
 
-    gzip *.headersRenamed_*.fq
+        gzip *.headersRenamed_*.fq
+        rm *.fq
 
-    rm *.fq
+        if [ "$clear" = "true" ];
+        then
+            work_regex=".*/work/.{2}/.{30}/.*"
+            file_source1=\$(readlink -f \$(pwd)/${fastq_pair[0]})
+            file_source2=\$(readlink -f \$(pwd)/${fastq_pair[1]})
+            if [[ "\$file_source1" =~ \$work_regex ]]; then
+                rm \$file_source1 \$file_source2
+            fi
+        fi
+
+    } || {
+        echo fail > .status
+    }
     """
 }
 
diff --git a/flowcraft/generator/templates/skesa.nf b/flowcraft/generator/templates/skesa.nf
index 8a3b0f13..d8852908 100644
--- a/flowcraft/generator/templates/skesa.nf
+++ b/flowcraft/generator/templates/skesa.nf
@@ -1,5 +1,5 @@
 
-clear = params.clearAtCheckpoint ? "true" : "false"
+clear = params.clearInput{{ param_id }} ? "true" : "false"
 checkpointClear_{{ pid }} = Channel.value(clear)
 
 process skesa_{{ pid }} {
diff --git a/flowcraft/generator/templates/spades.nf b/flowcraft/generator/templates/spades.nf
index b75afb8d..64b6e4c8 100644
--- a/flowcraft/generator/templates/spades.nf
+++ b/flowcraft/generator/templates/spades.nf
@@ -14,7 +14,7 @@ if ( params.spadesKmers{{ param_id }}.toString().split(" ").size() <= 1 ){
 }
 IN_spades_kmers_{{pid}} = Channel.value(params.spadesKmers{{ param_id }})
 
-clear = params.clearAtCheckpoint ? "true" : "false"
+clear = params.clearInput{{ param_id }} ? "true" : "false"
 checkpointClear_{{ pid }} = Channel.value(clear)
 
 process spades_{{ pid }} {
diff --git a/flowcraft/generator/templates/trimmomatic.nf b/flowcraft/generator/templates/trimmomatic.nf
index a13a9514..d096c814 100644
--- a/flowcraft/generator/templates/trimmomatic.nf
+++ b/flowcraft/generator/templates/trimmomatic.nf
@@ -15,7 +15,7 @@ if ( !params.trimMinLength{{ param_id}}.toString().isNumber() ){
 IN_trimmomatic_opts_{{ pid }} = Channel.value([params.trimSlidingWindow{{ param_id}},params.trimLeading{{ param_id}},params.trimTrailing{{ param_id}},params.trimMinLength{{ param_id}}])
 IN_adapters_{{ pid }} = Channel.value(params.adapters{{ param_id}})
 
-clear = params.clearAtCheckpoint ? "true" : "false"
+clear = params.clearInput{{ param_id }} ? "true" : "false"
 checkpointClear_{{ pid }} = Channel.value(clear)
 
 process trimmomatic_{{ pid }} {
diff --git a/flowcraft/generator/templates/viral_assembly.nf b/flowcraft/generator/templates/viral_assembly.nf
index 0a86be23..d4f90c44 100644
--- a/flowcraft/generator/templates/viral_assembly.nf
+++ b/flowcraft/generator/templates/viral_assembly.nf
@@ -22,8 +22,9 @@ if ( params.spadesKmers{{ param_id }}.toString().split(" ").size() <= 1 ){
     }
 }
 
-clear = params.clearAtCheckpoint ? "true" : "false"
-checkpointClear_{{ pid }} = Channel.value(clear)
+clear = params.clearInput{{ param_id }} ? "true" : "false"
+checkpointClearSpades_{{ pid }} = Channel.value(clear)
+checkpointClearMegahit_{{ pid }} = Channel.value(clear)
 
 //MEGAHIT OPTIONS
 if ( params.megahitKmers{{ param_id }}.toString().split(" ").size() <= 1 ){
@@ -57,7 +58,7 @@ process va_spades_{{ pid }} {
     set sample_id, file(fastq_pair), max_len from spades_in.join(SIDE_max_len_spades)
     val opts from IN_spades_opts_{{ pid }}
     val kmers from IN_spades_kmers_{{ pid }}
-    val clear from checkpointClear_{{ pid }}
+    val clear from checkpointClearSpades_{{ pid }}
 
     output:
     set sample_id, file({task.exitStatus == 1 ? ".exitcode" : '*_spades*.fasta'}) into assembly_spades
@@ -115,6 +116,7 @@ process va_megahit_{{ pid }}  {
     input:
     set sample_id, file(fastq_pair), max_len from megahit_in.join(megahit).map{ ot -> [ot[0], ot[1]] }.join(SIDE_max_len_megahit)
     val kmers from IN_megahit_kmers_{{ pid }}
+    val clear from checkpointClearSpades_{{ pid }}
 
     output:
     set sample_id, file('*megahit*.fasta') into megahit_assembly
diff --git a/flowcraft/templates/megahit.py b/flowcraft/templates/megahit.py
index b7e91830..6f7cefda 100644
--- a/flowcraft/templates/megahit.py
+++ b/flowcraft/templates/megahit.py
@@ -19,6 +19,8 @@
 - ``kmers`` : Setting for megahit kmers. Can be either ``'auto'``, \
     ``'default'`` or a user provided list. All must be odd, in the range 15-255, increment <= 28
     - e.g.: ``'auto'`` or ``'default'`` or ``'55 77 99 113 127'``
+- ``clear`` : If 'true', remove the input fastq files at the end of the
+    component run, IF THE FILES ARE IN THE WORK DIRECTORY
 
 Generated output
 ----------------
@@ -40,6 +42,7 @@
 __template__ = "megahit-nf"
 
 import os
+import re
 import subprocess
 
 from subprocess import PIPE
@@ -82,12 +85,14 @@ def __get_version_megahit():
     MAX_LEN = int('$max_len'.strip())
     KMERS = '$kmers'.strip()
     MEM = '$task.memory'
+    CLEAR = '$clear'
     logger.debug("Running {} with parameters:".format(
         os.path.basename(__file__)))
     logger.debug("SAMPLE_ID: {}".format(SAMPLE_ID))
     logger.debug("FASTQ_PAIR: {}".format(FASTQ_PAIR))
     logger.debug("MAX_LEN: {}".format(MAX_LEN))
     logger.debug("KMERS: {}".format(KMERS))
+    logger.debug("CLEAR: {}".format(CLEAR))
 
 
 def set_kmers(kmer_opt, max_read_len):
@@ -169,8 +174,27 @@ def fix_contig_names(asseembly_path):
     return fixed_assembly
 
 
+def clean_up(fastq):
+    """
+    Cleans the temporary fastq files. If they are symlinks, the link
+    source is removed
+
+    Parameters
+    ----------
+    fastq : list
+        List of fastq files.
+    """
+
+    for fq in fastq:
+        # Get real path of fastq files, following symlinks
+        rp = os.path.realpath(fq)
+        logger.debug("Removing temporary fastq file path: {}".format(rp))
+        if re.match(".*/work/.{2}/.{30}/.*", rp):
+            os.remove(rp)
+
+
 @MainWrapper
-def main(sample_id, fastq_pair, max_len, kmer, mem):
+def main(sample_id, fastq_pair, max_len, kmer, mem, clear):
     """Main executor of the megahit template.
 
     Parameters
@@ -264,7 +288,12 @@ def main(sample_id, fastq_pair, max_len, kmer, mem):
     os.rename(fixed_assembly, assembly_file)
     logger.info("Setting main assembly file to: {}".format(assembly_file))
 
+    # Remove input fastq files when clear option is specified.
+    # Only remove temporary input when the expected output exists.
+    if clear == "true" and os.path.exists(assembly_file):
+        clean_up(fastq_pair)
+
 
 if __name__ == '__main__':
 
-    main(SAMPLE_ID, FASTQ_PAIR, MAX_LEN, KMERS, MEM)
+    main(SAMPLE_ID, FASTQ_PAIR, MAX_LEN, KMERS, MEM, CLEAR)
diff --git a/flowcraft/templates/metaspades.py b/flowcraft/templates/metaspades.py
index d17d43d4..80a4d4db 100644
--- a/flowcraft/templates/metaspades.py
+++ b/flowcraft/templates/metaspades.py
@@ -40,6 +40,7 @@
 __template__ = "metaspades-nf"
 
 import os
+import re
 import subprocess
 
 from subprocess import PIPE
@@ -74,12 +75,33 @@ def __get_version_spades():
     FASTQ_PAIR = '$fastq_pair'.split()
     MAX_LEN = int('$max_len'.strip())
     KMERS = '$kmers'.strip()
+    CLEAR = '$clear'
     logger.debug("Running {} with parameters:".format(
         os.path.basename(__file__)))
     logger.debug("SAMPLE_ID: {}".format(SAMPLE_ID))
     logger.debug("FASTQ_PAIR: {}".format(FASTQ_PAIR))
     logger.debug("MAX_LEN: {}".format(MAX_LEN))
     logger.debug("KMERS: {}".format(KMERS))
+    logger.debug("CLEAR: {}".format(CLEAR))
+
+
+def clean_up(fastq):
+    """
+    Cleans the temporary fastq files. If they are symlinks, the link
+    source is removed
+
+    Parameters
+    ----------
+    fastq : list
+        List of fastq files.
+    """
+
+    for fq in fastq:
+        # Get real path of fastq files, following symlinks
+        rp = os.path.realpath(fq)
+        logger.debug("Removing temporary fastq file path: {}".format(rp))
+        if re.match(".*/work/.{2}/.{30}/.*", rp):
+            os.remove(rp)
 
 
 def set_kmers(kmer_opt, max_read_len):
@@ -129,7 +151,7 @@ def set_kmers(kmer_opt, max_read_len):
 
 
 @MainWrapper
-def main(sample_id, fastq_pair, max_len, kmer):
+def main(sample_id, fastq_pair, max_len, kmer, clear):
     """Main executor of the spades template.
 
     Parameters
@@ -211,7 +233,12 @@ def main(sample_id, fastq_pair, max_len, kmer):
     os.rename("contigs.fasta", assembly_file)
     logger.info("Setting main assembly file to: {}".format(assembly_file))
 
+    # Remove input fastq files when clear option is specified.
+    # Only remove temporary input when the expected output exists.
+    if clear == "true" and os.path.exists(assembly_file):
+        clean_up(fastq_pair)
+
 
 if __name__ == '__main__':
 
-    main(SAMPLE_ID, FASTQ_PAIR, MAX_LEN, KMERS)
+    main(SAMPLE_ID, FASTQ_PAIR, MAX_LEN, KMERS, CLEAR)
diff --git a/flowcraft/templates/spades.py b/flowcraft/templates/spades.py
index 32bd9e68..b283c6d9 100644
--- a/flowcraft/templates/spades.py
+++ b/flowcraft/templates/spades.py
@@ -258,7 +258,7 @@ def main(sample_id, fastq_pair, max_len, kmer, opts, clear):
 
     # Remove input fastq files when clear option is specified.
     # Only remove temporary input when the expected output exists.
-    if clear == "true" and os.path.exists("contigs.fasta"):
+    if clear == "true" and os.path.exists(assembly_file):
         clean_up(fastq_pair)
 
 
diff --git a/flowcraft/templates/trimmomatic.py b/flowcraft/templates/trimmomatic.py
index 7264bd1c..0ddc28fb 100644
--- a/flowcraft/templates/trimmomatic.py
+++ b/flowcraft/templates/trimmomatic.py
@@ -392,7 +392,9 @@ def main(sample_id, fastq_pair, trim_range, trim_opts, phred, adapters_file,
 
     trimmomatic_log("{}_trimlog.txt".format(sample_id), sample_id)
 
-    clean_up(fastq_pair, clear)
+    if p.returncode == 0 and os.path.exists("{}_1_trim.fastq.gz".format(
+            SAMPLE_ID)):
+        clean_up(fastq_pair, clear)
 
     # Check if trimmomatic ran successfully. If not, write the error message
     # to the status channel and exit.